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/7769818/working' mkdir: created directory `/scratch/stefan/7769818/working/protonate' Storing results in /scratch/stefan/7769818/finished Working in /scratch/stefan/7769818/working /scratch/stefan/7769818/working /scratch/stefan/7769818 /scratch/stefan/7769818/working/protonate /scratch/stefan/7769818/working /scratch/stefan/7769818 Precomputing protomers for all compounds (pH: 7.4) 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) 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 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 mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory Nov 27, 2019 6:18:26 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:26 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:56 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:25 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:55 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. ph 7.4: 1078 protomers created Coalesing and merging protomers 1028 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1028 protomers after new stereo-center expansion /scratch/stefan/7769818/working /scratch/stefan/7769818 Bulk generating 3D conformations all protomers in /scratch/stefan/7769818/working/3D mkdir: created directory `/scratch/stefan/7769818/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7769818/working/protonate/xaaaajd-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' 1029 3D conformations generated for 1000 compounds Building REAL300000237001 mkdir: created directory `/scratch/stefan/7769818/working/building' mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237001' /scratch/stefan/7769818/working/building/REAL300000237001 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237001 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237001/0 /scratch/stefan/7769818/working/building/REAL300000237001 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1 `/scratch/stefan/7769818/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000237001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237001 none CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [43, 43, 43, 43, 43, 17, 3, 17, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 2, 3, 3, 3, 3, 1, 1, 43, 43, 43, 43, 3, 3, 1, 1, 3, 3, 3, 3, 1, 1] 55 rigid atoms, others: [32, 37, 38, 9, 10, 11, 12, 13, 14, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 90 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237001 none CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 29, 5, 2, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 55, 55, 55, 55, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3] 55 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 122 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: REAL300000237001 none CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 13, 42, 42, 43, 43, 42, 42, 55, 55, 43, 43, 55, 55, 55, 55, 43, 43, 2, 2, 2, 1, 42, 42, 43, 43, 55, 55, 55, 55, 43, 43] 55 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 230 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237001 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237001 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `/scratch/stefan/7769818/finished' Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237001/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237001 Building REAL300000237002 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237002' /scratch/stefan/7769818/working/building/REAL300000237002 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237002 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237002/0 /scratch/stefan/7769818/working/building/REAL300000237002 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/2 `/scratch/stefan/7769818/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CN=NN2C)=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000237002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237002 none COC1=CC(C=CC(=O)C2=CN=NN2C)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 5, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 95, 95, 95, 33, 33, 10, 1, 10, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 175, 200, 200, 201, 201, 147, 147, 147, 95, 33, 33, 1, 2, 2, 2, 95, 200, 200, 200, 200] 201 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 538 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237002 none COC1=CC(C=CC(=O)C2=CN=NN2C)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 5, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 36, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 5, 13, 13, 21, 21, 3, 3, 3, 1, 5, 5, 95, 95, 95, 95, 1, 13, 14, 14, 14] 201 rigid atoms, others: [19, 1, 2, 3, 4, 5, 15, 16, 17, 18, 35, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 245 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237002 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237002 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237002/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237002 Building REAL300000237003 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237003' /scratch/stefan/7769818/working/building/REAL300000237003 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237003 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237003/0 /scratch/stefan/7769818/working/building/REAL300000237003 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/3 `/scratch/stefan/7769818/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=C(C(=O)[O-])C=C2)S1) `REAL300000237003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237003 none CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [158, 158, 158, 158, 158, 86, 13, 85, 13, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 6, 6, 7, 7, 1, 158, 158, 158, 158, 13, 13, 1, 1, 7, 7, 7, 7] 196 rigid atoms, others: [9, 10, 11, 12, 13, 14, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237003 none CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 196, 196, 196, 147, 60, 147, 60, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 196, 196, 196, 196, 60, 60, 7, 7, 1, 1, 1, 1] 196 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 457 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: REAL300000237003 none CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=C(C(=O)[O-])C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 12, 12, 52, 52, 158, 158, 158, 158, 196, 196, 182, 158, 196, 196, 196, 196, 158, 2, 2, 2, 1, 52, 52, 158, 158, 196, 196, 196, 196] 196 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 27] set([7, 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]) total number of confs: 568 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237003 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237003 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237003/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237003 Building REAL300000237004 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237004' /scratch/stefan/7769818/working/building/REAL300000237004 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237004 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237004/0 /scratch/stefan/7769818/working/building/REAL300000237004 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/4 `/scratch/stefan/7769818/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1) `REAL300000237004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237004 none CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 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: [123, 123, 123, 123, 123, 52, 12, 51, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 13, 13, 12, 1, 123, 123, 123, 123, 12, 12, 1, 1, 12, 12, 24, 12] 402 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237004 none CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 167, 74, 167, 74, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 74, 74, 12, 12, 1, 1, 2, 1] 402 rigid atoms, others: [33, 34, 36, 13, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 485 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: REAL300000237004 none CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=C(O)C(C(=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 48, 48, 123, 123, 123, 123, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 2, 2, 2, 1, 48, 48, 123, 123, 201, 201, 402, 201] 402 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 767 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237004 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237004 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237004/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237004 Building REAL300000237005 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237005' /scratch/stefan/7769818/working/building/REAL300000237005 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237005 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237005/0 /scratch/stefan/7769818/working/building/REAL300000237005 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/5 `/scratch/stefan/7769818/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1) `REAL300000237005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237005 none CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 113, 113, 113, 113, 56, 12, 55, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 12, 1, 113, 113, 113, 113, 13, 12, 1, 1, 12, 12, 12, 12] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237005 none CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 166, 77, 165, 77, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 78, 77, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 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: REAL300000237005 none CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=CC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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 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, 11, 11, 34, 34, 112, 112, 112, 112, 200, 200, 200, 201, 201, 201, 201, 201, 112, 2, 2, 2, 1, 34, 34, 113, 112, 200, 200, 200, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 27] set([7, 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]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237005 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237005 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237005/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237005 Building REAL300000237006 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237006' /scratch/stefan/7769818/working/building/REAL300000237006 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237006 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237006/0 /scratch/stefan/7769818/working/building/REAL300000237006 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/6 `/scratch/stefan/7769818/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1C(=O)C=CC1=CSC2=CC=C(C(=O)[O-])C=C12) `REAL300000237006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237006 none CN1N=NC=C1C(=O)C=CC1=CSC2=CC=C(C(=O)[O-])C=C12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 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, 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 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 80, 82, 82, 82, 54, 11, 54, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 11, 11, 1, 1, 1, 1] 82 rigid atoms, others: [9, 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, 22, 23, 24, 25, 26, 27]) total number of confs: 175 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237006 none CN1N=NC=C1C(=O)C=CC1=CSC2=CC=C(C(=O)[O-])C=C12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 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, 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 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, 12, 12, 44, 44, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 2, 2, 2, 1, 44, 44, 82, 82, 82, 82] 82 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 174 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237006 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237006 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237006/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237006 Building REAL300000237007 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237007' /scratch/stefan/7769818/working/building/REAL300000237007 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237007 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237007/0 /scratch/stefan/7769818/working/building/REAL300000237007 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/7 `/scratch/stefan/7769818/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1C(=O)C=CC1=CC(C(=O)[O-])=CC=C1Br) `REAL300000237007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237007 none CN1N=NC=C1C(=O)C=CC1=CC(C(=O)[O-])=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.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'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 7, 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, 7, 2, 2, 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, 45, 9, 45, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 9, 9, 1, 1, 1] 63 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25]) total number of confs: 141 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237007 none CN1N=NC=C1C(=O)C=CC1=CC(C(=O)[O-])=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.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'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 7, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 45, 45, 63, 63, 63, 63, 63, 63, 63, 63, 63, 2, 2, 2, 1, 45, 45, 63, 63, 63] 63 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 156 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237007 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237007 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237007/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237007 Building REAL300000237008 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237008' /scratch/stefan/7769818/working/building/REAL300000237008 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237008 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237008/0 /scratch/stefan/7769818/working/building/REAL300000237008 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/8 `/scratch/stefan/7769818/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1C(=O)C=CC1=CC=C(C(=O)[O-])C=C1[N+](=O)[O-]) `REAL300000237008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237008 none CN1N=NC=C1C(=O)C=CC1=CC=C(C(=O)[O-])C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 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, 33, 5, 33, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 55, 55, 55, 55, 5, 5, 1, 1, 1] 55 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237008 none CN1N=NC=C1C(=O)C=CC1=CC=C(C(=O)[O-])C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 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, 11, 11, 47, 47, 55, 55, 54, 55, 55, 55, 55, 55, 55, 55, 55, 2, 2, 2, 1, 47, 47, 55, 55, 55] 55 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237008 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237008 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237008/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237008 Building REAL300000237009 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237009' /scratch/stefan/7769818/working/building/REAL300000237009 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237009 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237009/0 /scratch/stefan/7769818/working/building/REAL300000237009 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/9 `/scratch/stefan/7769818/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=CC(C=CC(=O)C2=CN=NN2C)=C1OCC(=O)[O-]) `REAL300000237009.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237009 none COC1=CC(Br)=CC(C=CC(=O)C2=CN=NN2C)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [162, 111, 111, 111, 111, 111, 111, 42, 42, 13, 1, 13, 1, 1, 1, 1, 1, 1, 111, 111, 137, 192, 201, 201, 162, 162, 162, 111, 111, 42, 42, 1, 2, 2, 2, 192, 192] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 666 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237009 none COC1=CC(Br)=CC(C=CC(=O)C2=CN=NN2C)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 9, 9, 44, 44, 111, 111, 111, 111, 111, 1, 1, 3, 16, 30, 30, 4, 4, 4, 1, 1, 9, 9, 111, 111, 111, 111, 16, 16] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 297 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237009 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237009 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237009/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237009 Building REAL300000237010 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237010' /scratch/stefan/7769818/working/building/REAL300000237010 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237010 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237010/0 /scratch/stefan/7769818/working/building/REAL300000237010 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/10 `/scratch/stefan/7769818/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1C(=O)C=CC1=CC(I)=CC(C(=O)[O-])=C1) `REAL300000237010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237010 none CN1N=NC=C1C(=O)C=CC1=CC(I)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 7, 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, 7, 7, 7, 7, 2, 2, 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, 35, 5, 35, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 5, 5, 1, 1, 1] 59 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25]) total number of confs: 121 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237010 none CN1N=NC=C1C(=O)C=CC1=CC(I)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 7, 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, 7, 7, 7, 7, 2, 2, 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, 12, 12, 27, 27, 59, 59, 59, 59, 59, 59, 59, 59, 59, 2, 2, 2, 1, 27, 27, 59, 59, 59] 59 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 128 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237010 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237010 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237010/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237010 Building REAL300000237011 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237011' /scratch/stefan/7769818/working/building/REAL300000237011 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237011 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237011/0 /scratch/stefan/7769818/working/building/REAL300000237011 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/11 `/scratch/stefan/7769818/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1) `REAL300000237011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237011 none CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 23, 4, 23, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 20, 20, 5, 1, 1, 50, 50, 50, 50, 4, 4, 1, 1, 5, 5, 5, 9, 9, 5, 1, 1] 201 rigid atoms, others: [32, 33, 40, 9, 10, 11, 12, 13, 14, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 154 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237011 none CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 125, 125, 70, 13, 70, 13, 3, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 5, 5, 125, 125, 125, 125, 13, 13, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5] 201 rigid atoms, others: [34, 35, 36, 39, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 40, 41]) total number of confs: 278 number of broken/clashed sets: 11 ./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: REAL300000237011 none CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 39, 39, 50, 50, 40, 50, 125, 125, 120, 125, 125, 201, 201, 201, 125, 50, 50, 2, 2, 2, 1, 39, 39, 50, 50, 125, 125, 120, 201, 201, 125, 50, 50] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 757 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237011 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237011 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237011/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237011 Building REAL300000237012 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237012' /scratch/stefan/7769818/working/building/REAL300000237012 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237012 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237012/0 /scratch/stefan/7769818/working/building/REAL300000237012 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/12 `/scratch/stefan/7769818/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC(=O)C2=CN=NN2C)=CC=C1OCC(=O)[O-]) `REAL300000237012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237012 none CCOC1=CC(C=CC(=O)C2=CN=NN2C)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', '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, 5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 63, 27, 27, 27, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 108, 195, 196, 196, 87, 87, 87, 87, 87, 27, 7, 7, 1, 2, 2, 2, 27, 27, 195, 195] 201 rigid atoms, others: [32, 8, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 789 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237012 none CCOC1=CC(C=CC(=O)C2=CN=NN2C)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', '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, 5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 1, 1, 1, 1, 1, 5, 5, 13, 13, 27, 27, 27, 27, 27, 1, 1, 1, 1, 9, 37, 57, 57, 18, 18, 18, 18, 18, 1, 5, 5, 27, 27, 27, 27, 1, 1, 37, 37] 201 rigid atoms, others: [2, 3, 4, 5, 6, 16, 17, 18, 19, 36, 29, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 303 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237012 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237012 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237012/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237012 Building REAL300000237013 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237013' /scratch/stefan/7769818/working/building/REAL300000237013 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237013 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237013/0 /scratch/stefan/7769818/working/building/REAL300000237013 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/13 `/scratch/stefan/7769818/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CN=NN1C) `REAL300000237013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237013 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CN=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 5, 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, 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 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 42, 42, 13, 1, 13, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 56, 56, 42, 42, 1, 2, 2, 2] 56 rigid atoms, others: [33, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237013 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CN=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 5, 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, 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 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, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 39, 39, 56, 56, 56, 56, 56, 2, 2, 2, 1, 1, 1, 1, 9, 9, 56, 56, 56, 56] 56 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([32, 33, 34, 35, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 31]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237013 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237013 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237013/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237013 Building REAL300000237014 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237014' /scratch/stefan/7769818/working/building/REAL300000237014 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237014 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237014/0 /scratch/stefan/7769818/working/building/REAL300000237014 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/14 `/scratch/stefan/7769818/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1C(=O)C=CC1=CC=C(N2C=NC(C(=O)[O-])=C2)C=C1) `REAL300000237014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237014 none CN1N=NC=C1C(=O)C=CC1=CC=C(N2C=NC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', '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, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 48, 48, 48, 48, 23, 3, 23, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 48, 48, 48, 48, 3, 3, 1, 1, 11, 11, 1, 1] 80 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 98 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237014 none CN1N=NC=C1C(=O)C=CC1=CC=C(N2C=NC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', '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, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 60, 16, 60, 16, 10, 2, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 80, 80, 80, 80, 16, 16, 11, 11, 1, 1, 11, 11] 80 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 198 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: REAL300000237014 none CN1N=NC=C1C(=O)C=CC1=CC=C(N2C=NC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', '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, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 40, 40, 48, 48, 40, 48, 80, 80, 80, 80, 80, 80, 80, 48, 48, 2, 2, 2, 1, 40, 40, 48, 48, 80, 80, 48, 48] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 27] set([7, 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]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237014 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237014 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237014/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237014 Building REAL300000237015 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237015' /scratch/stefan/7769818/working/building/REAL300000237015 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237015 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237015/0 /scratch/stefan/7769818/working/building/REAL300000237015 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/15 `/scratch/stefan/7769818/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1C(=O)C=CC1=CC=C(OCC(=O)[O-])C(Cl)=C1) `REAL300000237015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237015 none CN1N=NC=C1C(=O)C=CC1=CC=C(OCC(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.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'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 7, 7, 7, 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, 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: [69, 69, 69, 69, 69, 36, 5, 36, 5, 1, 1, 1, 1, 1, 1, 9, 34, 59, 59, 1, 1, 1, 69, 69, 69, 69, 5, 5, 1, 1, 34, 34, 1] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 317 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237015 none CN1N=NC=C1C(=O)C=CC1=CC=C(OCC(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.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'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 7, 7, 7, 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, 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: [1, 1, 1, 1, 1, 1, 1, 5, 5, 25, 25, 69, 69, 69, 69, 164, 201, 201, 201, 69, 69, 69, 2, 2, 2, 1, 25, 25, 69, 69, 201, 201, 69] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 453 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237015 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237015 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237015/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237015 Building REAL300000237016 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237016' /scratch/stefan/7769818/working/building/REAL300000237016 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237016 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237016/0 /scratch/stefan/7769818/working/building/REAL300000237016 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/16 `/scratch/stefan/7769818/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1C(=O)C=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1) `REAL300000237016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237016 none CN1N=NC=C1C(=O)C=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', '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.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, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 6, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 11, 3, 11, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1, 1, 14, 14, 14, 14, 3, 3, 1, 1, 9, 17, 17, 1, 1] 55 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 105 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237016 none CN1N=NC=C1C(=O)C=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', '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.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, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 6, 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 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, 3, 3, 7, 8, 14, 14, 8, 14, 22, 22, 22, 43, 55, 55, 55, 14, 14, 2, 2, 2, 1, 7, 7, 14, 14, 43, 55, 55, 14, 14] 55 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 27] set([7, 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]) total number of confs: 263 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237016 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237016 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237016/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237016 Building REAL300000237017 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237017' /scratch/stefan/7769818/working/building/REAL300000237017 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237017 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237017/0 /scratch/stefan/7769818/working/building/REAL300000237017 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/17 `/scratch/stefan/7769818/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=CC=C2C(=O)[O-])C=C1) `REAL300000237017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237017 none CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=CC=C2C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 81, 25, 4, 25, 4, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 9, 9, 1, 1, 81, 81, 81, 81, 4, 4, 1, 1, 7, 7, 6, 7, 1, 1] 129 rigid atoms, others: [32, 37, 38, 9, 10, 11, 12, 13, 14, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 151 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237017 none CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=CC=C2C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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 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, 79, 15, 79, 15, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 129, 129, 129, 129, 15, 15, 7, 7, 1, 1, 1, 1, 7, 7] 129 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 290 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: REAL300000237017 none CN1N=NC=C1C(=O)C=CC1=CC=C(C2=CC=CC=C2C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 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 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 64, 64, 81, 81, 64, 67, 129, 129, 123, 129, 129, 129, 129, 129, 81, 81, 2, 2, 2, 1, 64, 64, 81, 81, 129, 129, 129, 129, 81, 81] 129 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 375 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237017 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237017 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237017/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237017 Building REAL300000237018 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237018' /scratch/stefan/7769818/working/building/REAL300000237018 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237018 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237018/0 /scratch/stefan/7769818/working/building/REAL300000237018 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/18 `/scratch/stefan/7769818/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1C(=O)C=CC1=C2C=C(C(=O)[O-])SC2=CC=C1F) `REAL300000237018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237018 none CN1N=NC=C1C(=O)C=CC1=C2C=C(C(=O)[O-])SC2=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 86, 86, 60, 9, 60, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 9, 9, 1, 1, 1] 86 rigid atoms, others: [9, 10, 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, 23, 24, 25, 26, 27, 28]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237018 none CN1N=NC=C1C(=O)C=CC1=C2C=C(C(=O)[O-])SC2=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 37, 37, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 2, 2, 2, 1, 37, 37, 86, 86, 86] 86 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237018 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237018 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237018/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237018 Building REAL300000237019 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237019' /scratch/stefan/7769818/working/building/REAL300000237019 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237019 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237019/0 /scratch/stefan/7769818/working/building/REAL300000237019 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/19 `/scratch/stefan/7769818/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)=CC=C1OCC(=O)[O-]) `REAL300000237019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237019 none COC1=CC(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 1, 29, 29, 29, 29, 99, 135, 140, 140, 49, 49, 49, 29, 11, 11, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 1, 29, 29, 135, 135] 201 rigid atoms, others: [34, 35, 36, 7, 9, 10, 11, 12, 13, 14, 45, 19] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49]) total number of confs: 450 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237019 none COC1=CC(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 29, 29, 13, 29, 29, 59, 65, 65, 65, 29, 1, 1, 1, 1, 9, 21, 29, 29, 3, 3, 3, 1, 5, 5, 29, 29, 15, 59, 59, 65, 65, 65, 65, 65, 65, 29, 1, 1, 21, 21] 201 rigid atoms, others: [1, 2, 3, 4, 5, 46, 47, 20, 21, 22, 23, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 393 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237019 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237019 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237019/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237019 Building REAL300000237020 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237020' /scratch/stefan/7769818/working/building/REAL300000237020 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237020 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237020/0 /scratch/stefan/7769818/working/building/REAL300000237020 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/20 `/scratch/stefan/7769818/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2)=C1) `REAL300000237020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237020 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 119, 119, 27, 119, 119, 27, 4, 27, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 119, 201, 201, 201, 201, 201, 201, 201, 201, 27, 119, 119, 4, 4, 1, 1, 1, 1, 119] 201 rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41]) total number of confs: 774 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237020 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 90, 90, 119, 119, 90, 90, 119, 119, 119, 119, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 90, 90, 119, 119, 119, 119, 1] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 41, 23] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 499 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237020 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237020 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237020/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237020 Building REAL300000237021 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237021' /scratch/stefan/7769818/working/building/REAL300000237021 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237021 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237021/0 /scratch/stefan/7769818/working/building/REAL300000237021 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/21 `/scratch/stefan/7769818/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(OCC(=O)[O-])C=C2)=C1) `REAL300000237021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237021 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(OCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 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] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 17, 17, 9, 17, 17, 7, 3, 7, 3, 1, 1, 1, 1, 1, 1, 5, 12, 14, 14, 1, 1, 17, 30, 30, 30, 30, 30, 30, 30, 30, 7, 17, 17, 3, 3, 1, 1, 12, 12, 1, 1, 17] 64 rigid atoms, others: [39, 40, 43, 44, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 45]) total number of confs: 154 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237021 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(OCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 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] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 17, 17, 13, 17, 29, 38, 40, 40, 17, 17, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 13, 13, 17, 17, 38, 38, 17, 17, 1] 64 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 45, 25, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 174 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237021 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237021 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237021/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237021 Building REAL300000237022 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237022' /scratch/stefan/7769818/working/building/REAL300000237022 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237022 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237022/0 /scratch/stefan/7769818/working/building/REAL300000237022 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/22 `/scratch/stefan/7769818/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(OCCC(=O)[O-])C=C2)=C1) `REAL300000237022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237022 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(OCCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 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] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 56, 62, 62, 19, 19, 7, 19, 19, 7, 3, 7, 3, 1, 1, 1, 1, 1, 1, 6, 16, 18, 28, 26, 1, 1, 19, 62, 62, 62, 62, 62, 62, 56, 56, 7, 19, 19, 3, 3, 1, 1, 16, 16, 18, 18, 1, 1, 19] 201 rigid atoms, others: [40, 41, 13, 14, 15, 16, 17, 18, 46, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 48]) total number of confs: 338 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237022 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(OCCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 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] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 19, 19, 13, 19, 84, 131, 135, 154, 146, 19, 19, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 11, 11, 19, 19, 131, 131, 135, 135, 19, 19, 1] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 48, 36, 26, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 536 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237022 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237022 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237022/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237022 Building REAL300000237023 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237023' /scratch/stefan/7769818/working/building/REAL300000237023 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237023 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237023/0 /scratch/stefan/7769818/working/building/REAL300000237023 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/23 `/scratch/stefan/7769818/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CC(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)=C1)C(=O)[O-]) `REAL300000237023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237023 none CC(OC1=CC=CC(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 7, 7, 7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 7, 8, 8, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 7] 8 rigid atoms, others: [36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 48]) total number of confs: 35 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237023 none CC(OC1=CC=CC(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 7, 7, 5, 7, 7, 8, 8, 8, 8, 7, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 7, 7, 5, 8, 8, 8, 8, 8, 8, 8, 8, 7, 1] 8 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 48, 23, 31] set([0, 1, 9, 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, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 34 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237023 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237023 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237023/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237023 Building REAL300000237024 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237024' /scratch/stefan/7769818/working/building/REAL300000237024 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237024 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237024/0 /scratch/stefan/7769818/working/building/REAL300000237024 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/24 `/scratch/stefan/7769818/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC(OCCC(=O)[O-])=C2)=C1) `REAL300000237024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237024 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC(OCCC(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 3, 5, 3, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 8, 8, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 8, 8, 3, 3, 1, 1, 1, 5, 5, 5, 5, 1, 8] 8 rigid atoms, others: [40, 41, 42, 13, 14, 15, 16, 17, 18, 19, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 48]) total number of confs: 57 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237024 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC(OCCC(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 5, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 1] 8 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 48, 36, 26, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 39 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237024 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237024 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237024/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237024 Building REAL300000237025 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237025' /scratch/stefan/7769818/working/building/REAL300000237025 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237025 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237025/0 /scratch/stefan/7769818/working/building/REAL300000237025 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/25 `/scratch/stefan/7769818/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)=C1) `REAL300000237025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237025 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 114, 120, 120, 67, 67, 67, 67, 67, 24, 9, 23, 9, 1, 1, 1, 1, 1, 1, 7, 7, 2, 2, 6, 7, 7, 7, 1, 67, 120, 120, 120, 120, 120, 120, 114, 114, 67, 67, 67, 9, 9, 1, 1, 7, 7, 7, 7, 67] 201 rigid atoms, others: [42, 43, 13, 14, 15, 16, 17, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 393 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237025 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 144, 144, 144, 144, 144, 72, 27, 72, 27, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 144, 201, 201, 201, 201, 201, 201, 201, 201, 144, 144, 144, 27, 27, 7, 7, 1, 1, 1, 1, 144] 201 rigid atoms, others: [44, 45, 46, 47, 17, 18, 19, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48]) total number of confs: 598 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: REAL300000237025 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 39, 39, 67, 67, 67, 67, 144, 144, 68, 67, 144, 144, 144, 144, 67, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 39, 39, 67, 67, 144, 144, 144, 144, 1] 201 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 39, 48, 38, 28, 5] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 708 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237025 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237025 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237025/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237025 Building REAL300000237026 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237026' /scratch/stefan/7769818/working/building/REAL300000237026 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237026 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237026/0 /scratch/stefan/7769818/working/building/REAL300000237026 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/26 `/scratch/stefan/7769818/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC(OCC(=O)[O-])=C2)=C1) `REAL300000237026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237026 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC(OCC(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 7, 7, 3, 7, 7, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 7, 9, 9, 9, 9, 9, 9, 9, 9, 3, 7, 7, 3, 3, 1, 1, 1, 3, 3, 1, 7] 9 rigid atoms, others: [39, 40, 41, 44, 13, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 45]) total number of confs: 36 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237026 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC(OCC(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1] 9 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 45, 25, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 30 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237026 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237026 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237026/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237026 Building REAL300000237027 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237027' /scratch/stefan/7769818/working/building/REAL300000237027 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237027 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237027/0 /scratch/stefan/7769818/working/building/REAL300000237027 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/27 `/scratch/stefan/7769818/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=C1) `REAL300000237027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237027 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 27, 29, 29, 15, 15, 9, 15, 15, 7, 3, 7, 3, 1, 1, 1, 1, 1, 1, 9, 27, 27, 27, 35, 35, 1, 1, 15, 29, 29, 29, 29, 29, 29, 27, 27, 7, 15, 15, 3, 3, 1, 1, 1, 1, 15] 95 rigid atoms, others: [41, 42, 43, 44, 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, 36, 37, 38, 39, 40, 45]) total number of confs: 232 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237027 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 8, 8, 11, 11, 15, 15, 11, 15, 41, 61, 61, 61, 69, 69, 15, 15, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 11, 11, 15, 15, 15, 15, 1] 95 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 45, 38, 4, 27, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237027 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237027 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237027/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237027 Building REAL300000237028 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237028' /scratch/stefan/7769818/working/building/REAL300000237028 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237028 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237028/0 /scratch/stefan/7769818/working/building/REAL300000237028 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/28 `/scratch/stefan/7769818/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)C=C1) `REAL300000237028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237028 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [51, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 1, 33, 33, 51, 51, 51, 33, 19, 19, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 1, 33, 33] 59 rigid atoms, others: [35, 36, 37, 46, 14, 16, 17, 18, 19, 20, 21, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 144 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237028 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 13, 13, 33, 33, 13, 33, 33, 57, 59, 59, 59, 33, 1, 1, 4, 4, 4, 1, 7, 7, 33, 33, 13, 57, 57, 59, 59, 59, 59, 59, 59, 33, 1, 1] 59 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 47, 48, 27, 28] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 250 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237028 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237028 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237028/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237028 Building REAL300000237029 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237029' /scratch/stefan/7769818/working/building/REAL300000237029 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237029 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237029/0 /scratch/stefan/7769818/working/building/REAL300000237029 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/29 `/scratch/stefan/7769818/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CN(CC(=O)[O-])N=N2)=C1) `REAL300000237029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237029 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CN(CC(=O)[O-])N=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [186, 178, 186, 186, 89, 89, 40, 89, 89, 40, 9, 39, 9, 1, 1, 1, 1, 1, 6, 12, 12, 1, 1, 89, 186, 186, 186, 186, 186, 186, 178, 178, 40, 89, 89, 9, 9, 1, 6, 6, 89] 201 rigid atoms, others: [37, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 754 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237029 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CN(CC(=O)[O-])N=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 11, 11, 43, 43, 89, 89, 89, 145, 159, 159, 89, 89, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 43, 43, 89, 145, 145, 1] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 40, 23] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 549 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237029 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237029 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237029/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237029 Building REAL300000237030 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237030' /scratch/stefan/7769818/working/building/REAL300000237030 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237030 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237030/0 /scratch/stefan/7769818/working/building/REAL300000237030 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/30 `/scratch/stefan/7769818/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2)=C1) `REAL300000237030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237030 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 35, 35, 17, 35, 35, 17, 5, 17, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 45, 45, 45, 45, 45, 45, 45, 45, 19, 35, 35, 5, 5, 1, 1, 1, 1, 35] 45 rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41]) total number of confs: 171 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237030 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 29, 29, 35, 35, 35, 35, 35, 35, 35, 35, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 29, 29, 35, 35, 35, 35, 1] 45 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 41, 23] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237030 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237030 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237030/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237030 Building REAL300000237031 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237031' /scratch/stefan/7769818/working/building/REAL300000237031 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237031 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237031/0 /scratch/stefan/7769818/working/building/REAL300000237031 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/31 `/scratch/stefan/7769818/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(C(=O)[O-])=CS2)=C1) `REAL300000237031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237031 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(C(=O)[O-])=CS2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 84, 84, 55, 84, 84, 51, 13, 51, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 84, 106, 106, 106, 106, 106, 106, 106, 106, 64, 84, 84, 13, 13, 1, 1, 84] 106 rigid atoms, others: [36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 359 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237031 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(C(=O)[O-])=CS2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 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, 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: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 41, 41, 84, 84, 84, 84, 84, 84, 84, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 41, 41, 84, 84, 1] 106 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 22, 38, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237031 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237031 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237031/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237031 Building REAL300000237032 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237032' /scratch/stefan/7769818/working/building/REAL300000237032 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237032 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237032/0 /scratch/stefan/7769818/working/building/REAL300000237032 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/32 `/scratch/stefan/7769818/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)=CC=C1OCCC(=O)[O-]) `REAL300000237032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237032 none COC1=CC(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 1, 26, 26, 26, 26, 85, 124, 126, 155, 148, 43, 43, 43, 26, 11, 11, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 1, 26, 26, 124, 124, 126, 126] 201 rigid atoms, others: [35, 36, 37, 7, 9, 10, 11, 12, 13, 14, 19, 46] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52]) total number of confs: 514 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237032 none COC1=CC(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 26, 26, 13, 26, 26, 52, 52, 52, 52, 26, 1, 1, 1, 1, 9, 29, 33, 41, 37, 3, 3, 3, 1, 5, 5, 26, 26, 15, 52, 52, 52, 52, 52, 52, 52, 52, 26, 1, 1, 29, 29, 33, 33] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 47, 48, 20, 21, 22, 23] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52]) total number of confs: 374 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237032 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237032 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237032/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237032 Building REAL300000237033 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237033' /scratch/stefan/7769818/working/building/REAL300000237033 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237033 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237033/0 /scratch/stefan/7769818/working/building/REAL300000237033 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/33 `/scratch/stefan/7769818/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2Cl)=C1) `REAL300000237033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237033 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 137, 137, 137, 137, 137, 56, 9, 56, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 137, 201, 201, 201, 201, 201, 201, 201, 201, 137, 137, 137, 9, 9, 1, 1, 1, 137] 201 rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41]) total number of confs: 612 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237033 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 57, 57, 137, 137, 84, 117, 137, 137, 137, 137, 137, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 57, 57, 137, 137, 137, 1] 201 rigid atoms, others: [33, 34, 35, 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, 32, 36, 37, 38, 39, 40]) total number of confs: 544 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237033 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237033 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237033/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237033 Building REAL300000237034 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237034' /scratch/stefan/7769818/working/building/REAL300000237034 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237034 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237034/0 /scratch/stefan/7769818/working/building/REAL300000237034 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/34 `/scratch/stefan/7769818/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2Cl)=C1) `REAL300000237034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237034 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 122, 122, 47, 122, 122, 47, 9, 47, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 122, 201, 201, 201, 201, 201, 201, 201, 201, 47, 122, 122, 9, 9, 1, 1, 1, 122] 201 rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41]) total number of confs: 738 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237034 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 46, 46, 122, 122, 122, 122, 122, 134, 134, 122, 122, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 46, 46, 122, 122, 122, 1] 201 rigid atoms, others: [33, 34, 35, 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, 32, 36, 37, 38, 39, 40]) total number of confs: 296 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237034 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237034 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237034/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237034 Building REAL300000237035 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237035' /scratch/stefan/7769818/working/building/REAL300000237035 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237035 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237035/0 /scratch/stefan/7769818/working/building/REAL300000237035 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/35 `/scratch/stefan/7769818/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(O)C(C(=O)[O-])=C2)=C1) `REAL300000237035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237035 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(O)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 354 conformations in input total number of sets (complete confs): 354 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 177, 120, 120, 54, 120, 120, 50, 6, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 120, 177, 177, 177, 177, 177, 177, 177, 177, 60, 120, 120, 6, 6, 1, 1, 2, 1, 120] 354 rigid atoms, others: [38, 39, 41, 13, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 42]) total number of confs: 683 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237035 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(O)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 354 conformations in input total number of sets (complete confs): 354 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 49, 49, 120, 120, 120, 120, 120, 120, 120, 120, 120, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 49, 49, 120, 120, 240, 120, 1] 354 rigid atoms, others: [33, 34, 35, 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, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 503 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237035 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237035 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237035/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237035 Building REAL300000237036 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237036' /scratch/stefan/7769818/working/building/REAL300000237036 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237036 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237036/0 /scratch/stefan/7769818/working/building/REAL300000237036 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/36 `/scratch/stefan/7769818/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(C[NH+](C)C)=C1) `REAL300000237036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237036 none CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(C[NH+](C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 1, 56, 56, 56, 56, 56, 56, 56, 56, 33, 33, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 1] 87 rigid atoms, others: [36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237036 none CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(C[NH+](C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 2, 2, 1, 1, 1, 7, 7, 31, 31, 56, 56, 31, 56, 56, 87, 87, 87, 87, 56, 2, 2, 2, 1, 2, 2, 2, 1, 7, 7, 56, 56, 34, 87, 87, 87, 87, 87, 87, 87, 87, 56] 87 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 29] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 351 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237036 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237036 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237036/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237036 Building REAL300000237037 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237037' /scratch/stefan/7769818/working/building/REAL300000237037 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237037 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237037/0 /scratch/stefan/7769818/working/building/REAL300000237037 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/37 `/scratch/stefan/7769818/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)C=C1)C(=O)[O-]) `REAL300000237037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237037 none CC(OC1=CC=C(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 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: [141, 103, 48, 38, 49, 49, 21, 21, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 1, 49, 49, 141, 150, 150, 141, 141, 141, 141, 49, 49, 21, 21, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 1, 49, 49] 201 rigid atoms, others: [35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 499 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237037 none CC(OC1=CC=C(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 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: [13, 6, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 49, 49, 20, 49, 49, 128, 138, 138, 138, 49, 1, 1, 13, 17, 17, 13, 13, 13, 13, 1, 1, 6, 6, 49, 49, 20, 128, 128, 138, 138, 138, 138, 138, 138, 49, 1, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 47, 48, 22, 23, 31] set([0, 1, 8, 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, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 597 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237037 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237037 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237037/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237037 Building REAL300000237038 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237038' /scratch/stefan/7769818/working/building/REAL300000237038 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237038 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237038/0 /scratch/stefan/7769818/working/building/REAL300000237038 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/38 `/scratch/stefan/7769818/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC=C2OCCC(=O)[O-])=C1) `REAL300000237038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237038 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC=C2OCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 5, 3, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 9, 9, 7, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 3, 3, 1, 1, 1, 1, 5, 5, 7, 7, 7] 13 rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48]) total number of confs: 66 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237038 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC=C2OCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 1, 5, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 1] 13 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 48, 36, 26, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 51 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237038 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237038 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237038/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237038 Building REAL300000237039 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237039' /scratch/stefan/7769818/working/building/REAL300000237039 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237039 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237039/0 /scratch/stefan/7769818/working/building/REAL300000237039 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/39 `/scratch/stefan/7769818/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)[O-])=C1C=CC(=O)C1=CC(C[NH+](C)C)=CC=C1) `REAL300000237039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237039 none CN1N=CC(C(=O)[O-])=C1C=CC(=O)C1=CC(C[NH+](C)C)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 19, 19, 19, 20, 20, 13, 13, 8, 1, 8, 1, 1, 1, 1, 4, 5, 5, 5, 1, 1, 1, 19, 19, 19, 19, 13, 13, 1, 4, 4, 5, 5, 5, 5, 5, 5, 1, 1, 1] 21 rigid atoms, others: [39, 40, 41, 11, 13, 14, 15, 16, 21, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237039 none CN1N=CC(C(=O)[O-])=C1C=CC(=O)C1=CC(C[NH+](C)C)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 7, 7, 11, 11, 19, 19, 19, 21, 21, 21, 21, 19, 19, 19, 2, 2, 2, 1, 7, 7, 19, 21, 21, 21, 21, 21, 21, 21, 21, 19, 19, 19] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 27] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237039 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237039 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237039/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237039 Building REAL300000237040 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237040' /scratch/stefan/7769818/working/building/REAL300000237040 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237040 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237040/0 /scratch/stefan/7769818/working/building/REAL300000237040 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/40 `/scratch/stefan/7769818/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])C(F)=C2)=C1) `REAL300000237040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237040 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])C(F)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 99, 99, 40, 99, 99, 40, 5, 40, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 99, 201, 201, 201, 201, 201, 201, 201, 201, 55, 99, 99, 5, 5, 1, 1, 1, 99] 201 rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41]) total number of confs: 762 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237040 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])C(F)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 35, 35, 99, 99, 99, 99, 135, 135, 99, 99, 99, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 35, 35, 99, 99, 99, 1] 201 rigid atoms, others: [33, 34, 35, 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, 32, 36, 37, 38, 39, 40]) total number of confs: 362 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237040 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237040 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237040/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237040 Building REAL300000237041 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237041' /scratch/stefan/7769818/working/building/REAL300000237041 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237041 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237041/0 /scratch/stefan/7769818/working/building/REAL300000237041 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/41 `/scratch/stefan/7769818/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C=CC(=O)[O-])O2)=C1) `REAL300000237041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237041 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C=CC(=O)[O-])O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [66, 60, 66, 66, 23, 23, 12, 23, 23, 12, 4, 11, 4, 1, 1, 1, 1, 1, 1, 8, 8, 19, 19, 1, 23, 66, 66, 66, 66, 66, 66, 60, 60, 12, 23, 23, 4, 4, 1, 1, 8, 8, 23] 75 rigid atoms, others: [38, 39, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237041 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C=CC(=O)[O-])O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 23, 23, 23, 23, 43, 43, 69, 69, 23, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 15, 15, 23, 23, 43, 43, 1] 75 rigid atoms, others: [33, 34, 35, 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, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237041 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237041 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237041/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237041 Building REAL300000237042 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237042' /scratch/stefan/7769818/working/building/REAL300000237042 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237042 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237042/0 /scratch/stefan/7769818/working/building/REAL300000237042 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/42 `/scratch/stefan/7769818/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)C=C1C(=O)[O-]) `REAL300000237042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237042 none COC1=CC=C(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)C=C1C(=O)[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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [35, 19, 19, 19, 19, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 1, 19, 19, 19, 27, 27, 35, 35, 35, 19, 19, 13, 13, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 1, 19] 63 rigid atoms, others: [33, 34, 35, 8, 44, 10, 11, 12, 13, 14, 15, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 45]) total number of confs: 138 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237042 none COC1=CC=C(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)C=C1C(=O)[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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 3, 3, 9, 9, 19, 19, 9, 19, 19, 47, 59, 59, 59, 19, 1, 1, 1, 3, 3, 4, 4, 4, 1, 1, 3, 3, 19, 19, 9, 47, 47, 59, 59, 59, 59, 59, 59, 19, 1] 63 rigid atoms, others: [1, 2, 3, 4, 5, 6, 45, 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, 41, 42, 43, 44]) total number of confs: 263 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237042 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237042 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237042/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237042 Building REAL300000237043 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237043' /scratch/stefan/7769818/working/building/REAL300000237043 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237043 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237043/0 /scratch/stefan/7769818/working/building/REAL300000237043 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/43 `/scratch/stefan/7769818/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(C(=O)[O-])=CC=C2F)=C1) `REAL300000237043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237043 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(C(=O)[O-])=CC=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 58, 58, 32, 58, 58, 32, 9, 32, 9, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 58, 82, 82, 82, 82, 82, 82, 82, 82, 32, 58, 58, 9, 9, 1, 1, 1, 58] 82 rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41]) total number of confs: 311 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237043 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(C(=O)[O-])=CC=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 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, 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: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 33, 33, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 33, 33, 58, 58, 58, 1] 82 rigid atoms, others: [33, 34, 35, 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, 32, 36, 37, 38, 39, 40]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237043 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237043 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237043/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237043 Building REAL300000237044 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237044' /scratch/stefan/7769818/working/building/REAL300000237044 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237044 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237044/0 /scratch/stefan/7769818/working/building/REAL300000237044 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/44 `/scratch/stefan/7769818/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(C[NH+](C)C)=C1) `REAL300000237044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237044 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(C[NH+](C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 51, 51, 51, 51, 51, 83, 51, 51, 75, 75, 51, 27, 27, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 1, 84, 84, 84, 51, 83, 83, 83, 51, 27, 27, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 1] 201 rigid atoms, others: [49, 38, 39, 40, 15, 17, 18, 19, 20, 21, 22, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 347 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237044 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(C[NH+](C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 3, 3, 1, 1, 1, 9, 9, 21, 21, 51, 51, 21, 51, 51, 101, 112, 112, 112, 51, 4, 4, 4, 1, 4, 4, 4, 1, 9, 9, 51, 51, 21, 101, 101, 112, 112, 112, 112, 112, 112, 51] 201 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 11, 12, 13, 35, 31] set([0, 6, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 473 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237044 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237044 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237044/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237044 Building REAL300000237045 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237045' /scratch/stefan/7769818/working/building/REAL300000237045 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237045 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237045/0 /scratch/stefan/7769818/working/building/REAL300000237045 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/45 `/scratch/stefan/7769818/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(F)C(C(=O)[O-])=C2)=C1) `REAL300000237045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237045 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 201, 201, 101, 101, 101, 101, 101, 42, 6, 42, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 101, 201, 201, 201, 201, 201, 201, 191, 191, 101, 101, 101, 6, 6, 1, 1, 1, 101] 201 rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41]) total number of confs: 673 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237045 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(F)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 45, 45, 101, 101, 101, 101, 101, 101, 147, 147, 101, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 45, 45, 101, 101, 101, 1] 201 rigid atoms, others: [33, 34, 35, 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, 32, 36, 37, 38, 39, 40]) total number of confs: 411 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237045 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237045 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237045/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237045 Building REAL300000237046 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237046' /scratch/stefan/7769818/working/building/REAL300000237046 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237046 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237046/0 /scratch/stefan/7769818/working/building/REAL300000237046 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/46 `/scratch/stefan/7769818/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(CC(=O)[O-])C=C2)=C1) `REAL300000237046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237046 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 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] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 162, 166, 166, 70, 70, 29, 70, 70, 23, 3, 23, 3, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 70, 166, 166, 166, 166, 166, 166, 162, 162, 39, 70, 70, 3, 3, 1, 1, 2, 2, 1, 1, 70] 201 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: 651 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237046 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 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] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 45, 45, 70, 70, 45, 45, 112, 143, 143, 70, 70, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 45, 45, 70, 70, 112, 112, 70, 70, 1] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 44, 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, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 680 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237046 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237046 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237046/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237046 Building REAL300000237047 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237047' /scratch/stefan/7769818/working/building/REAL300000237047 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237047 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237047/0 /scratch/stefan/7769818/working/building/REAL300000237047 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/47 `/scratch/stefan/7769818/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(Br)=CC(C(=O)[O-])=C2)=C1) `REAL300000237047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237047 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(Br)=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 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, 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, 35, 35, 35, 35, 35, 17, 5, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 51, 51, 51, 51, 51, 51, 51, 51, 35, 35, 35, 5, 5, 1, 1, 1, 35] 51 rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41]) total number of confs: 157 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237047 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(Br)=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 30, 30, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 30, 30, 35, 35, 35, 1] 51 rigid atoms, others: [33, 34, 35, 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, 32, 36, 37, 38, 39, 40]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237047 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237047 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237047/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237047 Building REAL300000237048 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237048' /scratch/stefan/7769818/working/building/REAL300000237048 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237048 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237048/0 /scratch/stefan/7769818/working/building/REAL300000237048 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/48 `/scratch/stefan/7769818/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])S2)=C1) `REAL300000237048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237048 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 122, 122, 70, 122, 122, 57, 13, 56, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 122, 173, 173, 173, 173, 173, 173, 173, 173, 82, 122, 122, 13, 13, 1, 1, 122] 173 rigid atoms, others: [36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 618 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237048 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 47, 47, 122, 122, 122, 122, 122, 122, 122, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 47, 47, 122, 122, 1] 173 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 22, 38, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237048 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237048 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237048/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237048 Building REAL300000237049 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237049' /scratch/stefan/7769818/working/building/REAL300000237049 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237049 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237049/0 /scratch/stefan/7769818/working/building/REAL300000237049 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/49 `/scratch/stefan/7769818/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C=CC(=O)[O-])C=C2)=C1) `REAL300000237049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237049 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C=CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 149, 162, 162, 59, 59, 20, 59, 59, 20, 3, 20, 3, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 1, 1, 59, 162, 162, 162, 162, 162, 162, 149, 149, 20, 59, 59, 3, 3, 1, 1, 5, 5, 1, 1, 59] 201 rigid atoms, others: [39, 40, 43, 44, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 45]) total number of confs: 687 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237049 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C=CC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 41, 41, 59, 59, 41, 41, 112, 112, 130, 130, 59, 59, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 41, 41, 59, 59, 112, 112, 59, 59, 1] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 45, 25, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 490 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237049 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237049 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237049/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237049 Building REAL300000237050 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237050' /scratch/stefan/7769818/working/building/REAL300000237050 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237050 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237050/0 /scratch/stefan/7769818/working/building/REAL300000237050 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/50 `/scratch/stefan/7769818/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(F)=C(C(=O)[O-])C=C2F)=C1) `REAL300000237050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237050 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(F)=C(C(=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 195, 201, 201, 111, 111, 38, 111, 111, 38, 11, 38, 11, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 111, 201, 201, 201, 201, 201, 201, 195, 195, 38, 111, 111, 11, 11, 1, 1, 111] 201 rigid atoms, others: [39, 40, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 759 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237050 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(F)=C(C(=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 36, 36, 111, 111, 111, 111, 111, 144, 144, 111, 111, 111, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 36, 36, 111, 111, 1] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 41, 25, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 358 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237050 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237050 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237050/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237050 Building REAL300000237051 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237051' /scratch/stefan/7769818/working/building/REAL300000237051 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237051 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237051/0 /scratch/stefan/7769818/working/building/REAL300000237051 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/51 `/scratch/stefan/7769818/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=C3C(=CC=C2)NN=C3C(=O)[O-])=C1) `REAL300000237051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237051 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=C3C(=CC=C2)NN=C3C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', '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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3] 3 rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237051 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=C3C(=CC=C2)NN=C3C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', '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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1] 3 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 44, 36, 26, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237051 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237051 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237051/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237051 Building REAL300000237052 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237052' /scratch/stefan/7769818/working/building/REAL300000237052 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237052 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237052/0 /scratch/stefan/7769818/working/building/REAL300000237052 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/52 `/scratch/stefan/7769818/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)=C1) `REAL300000237052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237052 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 114, 130, 130, 42, 42, 17, 42, 42, 17, 7, 17, 7, 1, 1, 1, 1, 1, 4, 10, 10, 1, 1, 1, 6, 6, 1, 6, 6, 42, 130, 130, 130, 130, 130, 130, 114, 114, 17, 42, 42, 7, 7, 1, 4, 4, 6, 6, 1, 6, 6, 42] 201 rigid atoms, others: [43, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 573 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237052 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [180, 172, 180, 180, 81, 81, 38, 81, 81, 38, 19, 38, 19, 6, 6, 6, 6, 6, 16, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 81, 180, 180, 180, 180, 180, 180, 172, 172, 38, 81, 81, 19, 19, 6, 16, 16, 1, 1, 1, 1, 1, 81] 201 rigid atoms, others: [46, 47, 48, 49, 50, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 51]) total number of confs: 811 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: REAL300000237052 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 42, 42, 42, 85, 101, 101, 42, 36, 42, 81, 81, 42, 81, 81, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 15, 15, 42, 85, 85, 81, 81, 42, 81, 81, 1] 201 rigid atoms, others: [4, 5, 38, 7, 8, 9, 10, 39, 40, 51, 6, 29] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 557 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237052 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237052 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237052/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237052 Building REAL300000237053 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237053' /scratch/stefan/7769818/working/building/REAL300000237053 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237053 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237053/0 /scratch/stefan/7769818/working/building/REAL300000237053 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/53 `/scratch/stefan/7769818/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C(O)=C3)O2)=C1) `REAL300000237053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237053 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C(O)=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 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: [82, 76, 82, 82, 31, 31, 14, 31, 31, 13, 4, 12, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 22, 22, 12, 12, 12, 1, 31, 82, 82, 82, 82, 82, 82, 76, 76, 16, 31, 31, 4, 4, 1, 1, 12, 12, 24, 12, 31] 402 rigid atoms, others: [43, 44, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49]) total number of confs: 397 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237053 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C(O)=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 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: [201, 185, 201, 201, 138, 138, 89, 138, 138, 87, 35, 86, 35, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 12, 138, 201, 201, 201, 201, 201, 201, 185, 185, 108, 138, 138, 35, 35, 12, 12, 1, 1, 2, 1, 138] 402 rigid atoms, others: [45, 46, 48, 17, 18, 19, 20, 21, 22, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 49]) total number of confs: 851 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: REAL300000237053 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C(O)=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 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: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 8, 8, 21, 21, 31, 31, 31, 31, 138, 138, 138, 138, 164, 164, 138, 138, 138, 31, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 21, 21, 31, 31, 138, 138, 276, 138, 1] 402 rigid atoms, others: [49, 4, 5, 38, 7, 8, 9, 10, 39, 40, 6, 29] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237053 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237053 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237053/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237053 Building REAL300000237054 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237054' /scratch/stefan/7769818/working/building/REAL300000237054 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237054 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237054/0 /scratch/stefan/7769818/working/building/REAL300000237054 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/54 `/scratch/stefan/7769818/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)=C1) `REAL300000237054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237054 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 140, 146, 146, 75, 75, 23, 75, 75, 23, 3, 23, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 3, 1, 1, 75, 146, 146, 146, 146, 146, 146, 140, 140, 39, 75, 75, 3, 3, 1, 1, 3, 3, 3, 3, 1, 1, 75] 201 rigid atoms, others: [50, 49, 43, 44, 13, 14, 15, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 51]) total number of confs: 614 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237054 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 130, 130, 43, 130, 130, 43, 5, 43, 5, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 130, 201, 201, 201, 201, 201, 201, 201, 201, 66, 130, 130, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 130] 201 rigid atoms, others: [46, 45, 48, 17, 18, 19, 20, 21, 22, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51]) total number of confs: 803 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: REAL300000237054 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 52, 52, 75, 75, 52, 56, 130, 130, 75, 75, 130, 130, 130, 130, 75, 75, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 52, 52, 75, 75, 130, 130, 130, 130, 75, 75, 1] 201 rigid atoms, others: [4, 5, 38, 7, 8, 9, 10, 39, 40, 51, 6, 29] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 786 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237054 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237054 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237054/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237054 Building REAL300000237055 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237055' /scratch/stefan/7769818/working/building/REAL300000237055 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237055 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237055/0 /scratch/stefan/7769818/working/building/REAL300000237055 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/55 `/scratch/stefan/7769818/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CNC3=CC=C(C(=O)[O-])C=C23)=C1) `REAL300000237055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237055 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CNC3=CC=C(C(=O)[O-])C=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5] 5 rigid atoms, others: [40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237055 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CNC3=CC=C(C(=O)[O-])C=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 1] 5 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 45, 36, 26, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237055 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237055 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237055/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237055 Building REAL300000237056 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237056' /scratch/stefan/7769818/working/building/REAL300000237056 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237056 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237056/0 /scratch/stefan/7769818/working/building/REAL300000237056 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/56 `/scratch/stefan/7769818/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])N=C2)=C1) `REAL300000237056.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237056 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 122, 122, 122, 122, 122, 42, 5, 42, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 201, 201, 201, 201, 201, 122, 122, 122, 5, 5, 1, 1, 1, 122] 201 rigid atoms, others: [37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40]) total number of confs: 631 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237056 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])N=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 58, 58, 122, 122, 122, 122, 122, 122, 122, 122, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 58, 58, 122, 122, 122, 1] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 40, 23] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 274 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237056 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237056 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237056/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237056 Building REAL300000237057 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237057' /scratch/stefan/7769818/working/building/REAL300000237057 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237057 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237057/0 /scratch/stefan/7769818/working/building/REAL300000237057 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/57 `/scratch/stefan/7769818/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])C(O)=C2)=C1) `REAL300000237057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237057 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])C(O)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 116, 116, 49, 116, 116, 41, 5, 41, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 116, 201, 201, 201, 201, 201, 201, 201, 201, 62, 116, 116, 5, 5, 1, 1, 2, 1, 116] 402 rigid atoms, others: [38, 39, 41, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 42]) total number of confs: 750 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237057 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])C(O)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 44, 44, 116, 116, 116, 116, 131, 131, 116, 116, 116, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 44, 44, 116, 116, 232, 116, 1] 402 rigid atoms, others: [33, 34, 35, 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, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 541 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237057 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237057 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237057/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237057 Building REAL300000237058 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237058' /scratch/stefan/7769818/working/building/REAL300000237058 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237058 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237058/0 /scratch/stefan/7769818/working/building/REAL300000237058 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/58 `/scratch/stefan/7769818/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)C=C1C(=O)[O-]) `REAL300000237058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237058 none CC1=CC=C(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [39, 39, 39, 39, 29, 29, 8, 1, 8, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 1, 39, 39, 39, 55, 55, 39, 39, 39, 39, 39, 29, 29, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 1, 39] 79 rigid atoms, others: [32, 33, 34, 43, 7, 9, 10, 11, 12, 13, 14, 19] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 44]) total number of confs: 186 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237058 none CC1=CC=C(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 39, 39, 17, 39, 39, 77, 79, 79, 79, 39, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 5, 5, 39, 39, 17, 77, 77, 79, 79, 79, 79, 79, 79, 39, 1] 79 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 20, 21, 22, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 309 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237058 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237058 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237058/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237058 Building REAL300000237059 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237059' /scratch/stefan/7769818/working/building/REAL300000237059 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237059 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237059/0 /scratch/stefan/7769818/working/building/REAL300000237059 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/59 `/scratch/stefan/7769818/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(C(=O)[O-])=C(Cl)S2)=C1) `REAL300000237059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237059 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(C(=O)[O-])=C(Cl)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 201, 92, 92, 92, 92, 92, 38, 13, 37, 13, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 92, 201, 201, 201, 201, 201, 201, 193, 193, 92, 92, 92, 13, 13, 1, 92] 201 rigid atoms, others: [37, 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, 35, 36, 38]) total number of confs: 703 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237059 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(C(=O)[O-])=C(Cl)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 18, 18, 92, 92, 92, 144, 144, 92, 92, 92, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 18, 18, 92, 1] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 23, 38] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237059 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237059 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237059/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237059 Building REAL300000237060 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237060' /scratch/stefan/7769818/working/building/REAL300000237060 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237060 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237060/0 /scratch/stefan/7769818/working/building/REAL300000237060 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/60 `/scratch/stefan/7769818/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)O1) `REAL300000237060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237060 none CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', '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, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 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: [99, 99, 99, 99, 134, 134, 99, 43, 43, 11, 1, 11, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 1, 99, 99, 99, 99, 99, 43, 43, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 1] 201 rigid atoms, others: [32, 41, 10, 12, 13, 14, 15, 16, 17, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 365 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237060 none CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', '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, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 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, 3, 3, 1, 1, 1, 9, 9, 34, 34, 99, 99, 34, 99, 99, 191, 201, 201, 201, 99, 1, 2, 2, 2, 1, 9, 9, 99, 99, 34, 191, 191, 201, 201, 201, 201, 201, 201, 99] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 23, 27] set([4, 5, 9, 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, 38, 39, 40, 41]) total number of confs: 790 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237060 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237060 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237060/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237060 Building REAL300000237061 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237061' /scratch/stefan/7769818/working/building/REAL300000237061 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237061 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237061/0 /scratch/stefan/7769818/working/building/REAL300000237061 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/61 `/scratch/stefan/7769818/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)=C1) `REAL300000237061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237061 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 155, 161, 161, 83, 83, 43, 83, 83, 43, 12, 42, 12, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 6, 1, 83, 161, 161, 161, 161, 161, 161, 155, 155, 48, 83, 83, 12, 12, 1, 1, 6, 6, 6, 6, 83] 201 rigid atoms, others: [42, 43, 13, 14, 15, 16, 17, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 650 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237061 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 155, 155, 85, 155, 155, 85, 40, 85, 40, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 155, 201, 201, 201, 201, 201, 201, 201, 201, 95, 155, 155, 40, 40, 6, 6, 1, 1, 1, 1, 155] 201 rigid atoms, others: [44, 45, 46, 47, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48]) total number of confs: 745 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: REAL300000237061 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 11, 11, 29, 29, 83, 83, 83, 83, 155, 155, 83, 83, 155, 155, 155, 155, 83, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 29, 29, 83, 83, 155, 155, 155, 155, 1] 201 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 39, 48, 38, 28, 5] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 704 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237061 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237061 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237061/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237061 Building REAL300000237062 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237062' /scratch/stefan/7769818/working/building/REAL300000237062 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237062 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237062/0 /scratch/stefan/7769818/working/building/REAL300000237062 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/62 `/scratch/stefan/7769818/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=CC(C[NH+](C)C)=CC=C1) `REAL300000237062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237062 none CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=CC(C[NH+](C)C)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [75, 75, 75, 75, 75, 75, 75, 75, 34, 34, 13, 1, 13, 1, 1, 1, 1, 6, 9, 9, 9, 1, 1, 1, 75, 75, 75, 75, 34, 34, 1, 6, 6, 9, 9, 9, 9, 9, 9, 1, 1, 1] 99 rigid atoms, others: [39, 40, 41, 11, 13, 14, 15, 16, 21, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 182 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237062 none CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=CC(C[NH+](C)C)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 10, 10, 37, 37, 75, 75, 75, 99, 99, 99, 99, 51, 75, 75, 2, 2, 2, 1, 10, 10, 75, 99, 99, 99, 99, 99, 99, 99, 99, 51, 75, 75] 99 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237062 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237062 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237062/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237062 Building REAL300000237063 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237063' /scratch/stefan/7769818/working/building/REAL300000237063 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237063 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237063/0 /scratch/stefan/7769818/working/building/REAL300000237063 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/63 `/scratch/stefan/7769818/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1) `REAL300000237063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237063 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 16, 16, 8, 16, 16, 8, 4, 7, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 4, 3, 1, 16, 29, 29, 29, 29, 29, 29, 29, 29, 8, 16, 16, 4, 4, 1, 1, 3, 3, 6, 3, 16] 58 rigid atoms, others: [43, 44, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237063 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 23, 23, 14, 23, 23, 14, 10, 13, 10, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 3, 23, 29, 29, 29, 29, 29, 29, 29, 29, 14, 23, 23, 10, 10, 3, 3, 1, 1, 2, 1, 23] 58 rigid atoms, others: [45, 46, 48, 17, 18, 19, 20, 21, 22, 23, 24, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 49]) total number of confs: 113 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: REAL300000237063 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 16, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 16, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 10, 10, 16, 16, 23, 23, 46, 23, 1] 58 rigid atoms, others: [49, 4, 5, 38, 7, 8, 9, 10, 39, 40, 6, 29] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237063 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237063 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237063/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237063 Building REAL300000237064 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237064' /scratch/stefan/7769818/working/building/REAL300000237064 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237064 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237064/0 /scratch/stefan/7769818/working/building/REAL300000237064 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/64 `/scratch/stefan/7769818/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CN=CC(C(=O)[O-])=C2)=C1) `REAL300000237064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237064 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CN=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 36, 36, 36, 36, 36, 20, 6, 20, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 48, 48, 48, 48, 48, 48, 48, 48, 36, 36, 36, 6, 6, 1, 1, 1, 36] 48 rigid atoms, others: [37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40]) total number of confs: 139 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237064 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CN=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 29, 29, 36, 36, 36, 36, 36, 36, 36, 36, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 29, 29, 36, 36, 36, 1] 48 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 40, 23] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237064 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237064 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237064/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237064 Building REAL300000237065 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237065' /scratch/stefan/7769818/working/building/REAL300000237065 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237065 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237065/0 /scratch/stefan/7769818/working/building/REAL300000237065 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/65 `/scratch/stefan/7769818/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=C1) `REAL300000237065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237065 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 157, 159, 159, 81, 81, 42, 81, 81, 42, 12, 41, 12, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 10, 10, 9, 1, 81, 159, 159, 159, 159, 159, 159, 157, 157, 43, 81, 81, 12, 12, 1, 1, 9, 9, 9, 9, 81] 201 rigid atoms, others: [42, 43, 13, 14, 15, 16, 17, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 600 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237065 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 157, 157, 115, 157, 157, 115, 59, 115, 59, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 157, 201, 201, 201, 201, 201, 201, 201, 201, 120, 157, 157, 59, 59, 9, 9, 1, 1, 1, 1, 157] 201 rigid atoms, others: [44, 45, 46, 47, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48]) total number of confs: 711 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: REAL300000237065 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 31, 31, 81, 81, 81, 81, 157, 157, 157, 157, 157, 157, 157, 157, 81, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 31, 31, 81, 81, 157, 157, 157, 157, 1] 201 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 39, 48, 38, 28, 5] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237065 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237065 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237065/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237065 Building REAL300000237066 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237066' /scratch/stefan/7769818/working/building/REAL300000237066 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237066 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237066/0 /scratch/stefan/7769818/working/building/REAL300000237066 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/66 `/scratch/stefan/7769818/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(C[NH+](C)C)=C1) `REAL300000237066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237066 none COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(C[NH+](C)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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [107, 73, 73, 73, 73, 73, 73, 73, 73, 73, 33, 33, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 1, 107, 107, 107, 73, 73, 73, 33, 33, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 1] 127 rigid atoms, others: [34, 35, 36, 45, 13, 15, 16, 17, 18, 19, 20, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 234 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237066 none COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(C[NH+](C)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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 39, 39, 73, 73, 39, 73, 73, 121, 127, 127, 127, 73, 3, 3, 3, 1, 1, 1, 9, 9, 73, 73, 39, 121, 121, 127, 127, 127, 127, 127, 127, 73] 127 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, 42, 43, 44, 45]) total number of confs: 508 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237066 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237066 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237066/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237066 Building REAL300000237067 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237067' /scratch/stefan/7769818/working/building/REAL300000237067 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237067 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237067/0 /scratch/stefan/7769818/working/building/REAL300000237067 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/67 `/scratch/stefan/7769818/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CSC3=CC=C(C(=O)[O-])C=C23)=C1) `REAL300000237067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237067 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CSC3=CC=C(C(=O)[O-])C=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 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, 1, 7, 7, 7, 7, 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, 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, 4, 8, 8, 4, 3, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 8, 8, 3, 3, 1, 1, 1, 1, 8] 8 rigid atoms, others: [40, 41, 42, 43, 13, 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, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237067 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CSC3=CC=C(C(=O)[O-])C=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 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, 1, 7, 7, 7, 7, 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, 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, 4, 7, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 1] 8 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 44, 36, 26, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237067 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237067 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237067/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237067 Building REAL300000237068 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237068' /scratch/stefan/7769818/working/building/REAL300000237068 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237068 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237068/0 /scratch/stefan/7769818/working/building/REAL300000237068 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/68 `/scratch/stefan/7769818/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(C(=O)[O-])=CC=C2Br)=C1) `REAL300000237068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237068 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(C(=O)[O-])=CC=C2Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 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, 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, 51, 51, 33, 51, 51, 27, 7, 27, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 51, 71, 71, 71, 71, 71, 71, 71, 71, 33, 51, 51, 7, 7, 1, 1, 1, 51] 71 rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41]) total number of confs: 253 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237068 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(C(=O)[O-])=CC=C2Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 8, 8, 32, 32, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 32, 32, 51, 51, 51, 1] 71 rigid atoms, others: [33, 34, 35, 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, 32, 36, 37, 38, 39, 40]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237068 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237068 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237068/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237068 Building REAL300000237069 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237069' /scratch/stefan/7769818/working/building/REAL300000237069 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237069 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237069/0 /scratch/stefan/7769818/working/building/REAL300000237069 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/69 `/scratch/stefan/7769818/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2[N+](=O)[O-])=C1) `REAL300000237069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237069 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2[N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 129, 129, 59, 129, 129, 36, 5, 36, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 129, 201, 201, 201, 201, 201, 201, 201, 201, 60, 129, 129, 5, 5, 1, 1, 1, 129] 201 rigid atoms, others: [40, 41, 42, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43]) total number of confs: 756 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237069 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2[N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 76, 76, 129, 129, 95, 95, 129, 129, 129, 129, 129, 129, 129, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 76, 76, 129, 129, 129, 1] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 43, 36, 26, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 537 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237069 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237069 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237069/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237069 Building REAL300000237070 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237070' /scratch/stefan/7769818/working/building/REAL300000237070 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237070 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237070/0 /scratch/stefan/7769818/working/building/REAL300000237070 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/70 `/scratch/stefan/7769818/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC(CC(=O)[O-])=C2)=C1) `REAL300000237070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237070 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC(CC(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 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, 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, 89, 95, 95, 57, 57, 23, 57, 57, 23, 5, 23, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 57, 95, 95, 95, 95, 95, 95, 89, 89, 23, 57, 57, 5, 5, 1, 1, 1, 2, 2, 1, 57] 95 rigid atoms, others: [38, 39, 40, 43, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 44]) total number of confs: 395 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237070 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC(CC(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 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, 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: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 34, 34, 57, 57, 40, 57, 57, 57, 77, 77, 57, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 34, 34, 57, 57, 57, 57, 57, 57, 1] 95 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 44, 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, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 317 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237070 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237070 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237070/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237070 Building REAL300000237071 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237071' /scratch/stefan/7769818/working/building/REAL300000237071 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237071 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237071/0 /scratch/stefan/7769818/working/building/REAL300000237071 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/71 `/scratch/stefan/7769818/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)=CC=C1C(=O)[O-]) `REAL300000237071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237071 none COC1=CC(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 71, 71, 71, 31, 31, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 1, 71, 71, 71, 71, 93, 93, 101, 101, 101, 71, 31, 31, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 1, 71, 71] 201 rigid atoms, others: [32, 33, 34, 43, 7, 9, 10, 11, 12, 13, 14, 19] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 323 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237071 none COC1=CC(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 71, 71, 17, 71, 71, 163, 173, 173, 173, 71, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 5, 5, 71, 71, 18, 163, 163, 173, 173, 173, 173, 173, 173, 71, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 44, 45, 20, 21, 22, 23, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 669 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237071 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237071 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237071/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237071 Building REAL300000237072 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237072' /scratch/stefan/7769818/working/building/REAL300000237072 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237072 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237072/0 /scratch/stefan/7769818/working/building/REAL300000237072 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/72 `/scratch/stefan/7769818/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=C(F)C=C(C(=O)[O-])C=C2F)=C1) `REAL300000237072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237072 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=C(F)C=C(C(=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 124, 124, 124, 124, 124, 50, 7, 50, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 124, 201, 201, 201, 201, 201, 201, 201, 201, 124, 124, 124, 7, 7, 1, 1, 124] 201 rigid atoms, others: [39, 40, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 657 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237072 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=C(F)C=C(C(=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 54, 55, 121, 121, 121, 55, 74, 121, 121, 121, 121, 121, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 54, 54, 121, 121, 1] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 41, 25, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 593 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237072 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237072 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237072/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237072 Building REAL300000237073 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237073' /scratch/stefan/7769818/working/building/REAL300000237073 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237073 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237073/0 /scratch/stefan/7769818/working/building/REAL300000237073 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/73 `/scratch/stefan/7769818/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=C(F)C=CC(C(=O)[O-])=C2F)=C1) `REAL300000237073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237073 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=C(F)C=CC(C(=O)[O-])=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 201, 201, 105, 105, 41, 105, 105, 41, 11, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 105, 201, 201, 201, 201, 201, 201, 197, 197, 44, 105, 105, 11, 11, 1, 1, 105] 201 rigid atoms, others: [39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 740 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237073 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=C(F)C=CC(C(=O)[O-])=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 34, 34, 105, 105, 105, 105, 105, 105, 147, 147, 105, 105, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 34, 34, 105, 105, 1] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 41, 25, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237073 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237073 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237073/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237073 Building REAL300000237074 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237074' /scratch/stefan/7769818/working/building/REAL300000237074 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237074 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237074/0 /scratch/stefan/7769818/working/building/REAL300000237074 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/74 `/scratch/stefan/7769818/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=C1) `REAL300000237074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237074 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 121, 122, 122, 59, 59, 23, 59, 59, 23, 3, 23, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 18, 18, 5, 1, 1, 59, 122, 122, 122, 122, 122, 122, 121, 121, 32, 59, 59, 3, 3, 1, 1, 5, 5, 5, 9, 9, 5, 1, 1, 59] 201 rigid atoms, others: [45, 44, 13, 14, 15, 16, 17, 18, 52, 53, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51, 54]) total number of confs: 536 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237074 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 186, 186, 112, 112, 48, 112, 112, 48, 9, 48, 9, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 5, 5, 112, 186, 186, 186, 186, 186, 186, 186, 186, 64, 112, 112, 9, 9, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5, 112] 201 rigid atoms, others: [51, 47, 48, 17, 18, 19, 20, 46, 22, 23, 27, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 49, 50, 52, 53, 54]) total number of confs: 755 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: REAL300000237074 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 11, 11, 39, 39, 59, 59, 53, 59, 112, 112, 109, 112, 112, 127, 143, 143, 112, 59, 59, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 39, 39, 59, 59, 112, 112, 112, 127, 127, 112, 59, 59, 1] 201 rigid atoms, others: [4, 5, 6, 39, 8, 9, 10, 7, 40, 54, 41, 30] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 466 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237074 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237074 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237074/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237074 Building REAL300000237075 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237075' /scratch/stefan/7769818/working/building/REAL300000237075 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237075 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237075/0 /scratch/stefan/7769818/working/building/REAL300000237075 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/75 `/scratch/stefan/7769818/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CSC(C(=O)[O-])=C2)=C1) `REAL300000237075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237075 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CSC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 59, 59, 59, 59, 59, 29, 6, 29, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 59, 82, 82, 82, 82, 82, 82, 82, 82, 59, 59, 59, 6, 6, 1, 1, 59] 82 rigid atoms, others: [36, 37, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237075 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CSC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 40, 40, 59, 59, 59, 59, 59, 59, 59, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 40, 40, 59, 59, 1] 82 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 22, 38, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237075 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237075 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237075/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237075 Building REAL300000237076 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237076' /scratch/stefan/7769818/working/building/REAL300000237076 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237076 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237076/0 /scratch/stefan/7769818/working/building/REAL300000237076 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/76 `/scratch/stefan/7769818/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)=CC=C1OCC(=O)[O-]) `REAL300000237076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237076 none CCOC1=CC(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 25, 25, 25, 10, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 1, 25, 25, 25, 25, 95, 143, 143, 143, 49, 49, 49, 49, 49, 25, 10, 10, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 1, 25, 25, 143, 143] 201 rigid atoms, others: [37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 48, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 520 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237076 none CCOC1=CC(C=CC(=O)C2=CC=CC(C[NH+](C)C)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 5, 5, 13, 13, 25, 25, 13, 25, 25, 54, 55, 55, 55, 25, 1, 1, 1, 1, 7, 19, 21, 21, 5, 5, 5, 5, 5, 1, 5, 5, 25, 25, 13, 54, 54, 55, 55, 55, 55, 55, 55, 25, 1, 1, 19, 19] 201 rigid atoms, others: [34, 3, 4, 5, 6, 2, 49, 50, 21, 22, 23, 24] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52]) total number of confs: 320 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237076 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237076 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237076/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237076 Building REAL300000237077 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237077' /scratch/stefan/7769818/working/building/REAL300000237077 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237077 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237077/0 /scratch/stefan/7769818/working/building/REAL300000237077 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/77 `/scratch/stefan/7769818/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(F)=C(C(=O)[O-])C(F)=C2)=C1) `REAL300000237077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237077 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(F)=C(C(=O)[O-])C(F)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 201, 201, 88, 88, 26, 88, 88, 21, 3, 21, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 88, 201, 201, 201, 201, 201, 201, 192, 192, 36, 88, 88, 3, 3, 1, 1, 88] 201 rigid atoms, others: [39, 40, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 782 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237077 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC(F)=C(C(=O)[O-])C(F)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 60, 60, 93, 93, 93, 60, 93, 127, 127, 93, 93, 93, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 60, 60, 93, 93, 1] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 41, 25, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 545 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237077 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237077 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237077/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237077 Building REAL300000237078 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237078' /scratch/stefan/7769818/working/building/REAL300000237078 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237078 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237078/0 /scratch/stefan/7769818/working/building/REAL300000237078 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/78 `/scratch/stefan/7769818/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC3=C(C=C(C(=O)[O-])N3)O2)=C1) `REAL300000237078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237078 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC3=C(C=C(C(=O)[O-])N3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 134, 134, 67, 134, 134, 53, 12, 53, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 134, 201, 201, 201, 201, 201, 201, 201, 201, 78, 134, 134, 12, 12, 1, 1, 1, 134] 201 rigid atoms, others: [39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42]) total number of confs: 782 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237078 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC3=C(C=C(C(=O)[O-])N3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 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: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 64, 64, 134, 134, 134, 134, 134, 134, 134, 134, 134, 134, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 64, 64, 134, 134, 134, 1] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 25, 42, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237078 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237078 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237078/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237078 Building REAL300000237079 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237079' /scratch/stefan/7769818/working/building/REAL300000237079 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237079 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237079/0 /scratch/stefan/7769818/working/building/REAL300000237079 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/79 `/scratch/stefan/7769818/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)=C1) `REAL300000237079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237079 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', '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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 122, 122, 67, 122, 122, 43, 6, 43, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 122, 201, 201, 201, 201, 201, 201, 201, 201, 63, 122, 122, 6, 6, 1, 1, 1, 1, 122] 201 rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44]) total number of confs: 771 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237079 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', '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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 61, 61, 122, 122, 122, 122, 122, 122, 122, 122, 122, 122, 122, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 61, 61, 122, 122, 122, 122, 1] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 44, 36, 26, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 276 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237079 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237079 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237079/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237079 Building REAL300000237080 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237080' /scratch/stefan/7769818/working/building/REAL300000237080 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237080 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237080/0 /scratch/stefan/7769818/working/building/REAL300000237080 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/80 `/scratch/stefan/7769818/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CN3C(C(=O)[O-])=CN=C23)=C1) `REAL300000237080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237080 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CN3C(C(=O)[O-])=CN=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 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, 1, 7, 7, 7, 7, 7, 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, 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, 43, 43, 25, 43, 43, 25, 9, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 52, 52, 52, 52, 52, 52, 52, 52, 25, 43, 43, 9, 9, 1, 1, 1, 1, 43] 52 rigid atoms, others: [40, 41, 42, 43, 13, 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, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44]) total number of confs: 176 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237080 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CN3C(C(=O)[O-])=CN=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 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, 1, 7, 7, 7, 7, 7, 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, 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: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 8, 8, 25, 25, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 25, 25, 43, 43, 43, 43, 1] 52 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 44, 36, 26, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237080 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237080 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237080/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237080 Building REAL300000237081 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237081' /scratch/stefan/7769818/working/building/REAL300000237081 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237081 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237081/0 /scratch/stefan/7769818/working/building/REAL300000237081 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/81 `/scratch/stefan/7769818/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CC=CC(C[NH+](C)C)=C1) `REAL300000237081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237081 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CC=CC(C[NH+](C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 51, 51, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 1, 141, 141, 141, 141, 141, 141, 141, 51, 51, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 1] 201 rigid atoms, others: [38, 39, 40, 16, 49, 18, 19, 20, 21, 22, 23, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237081 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CC=CC(C[NH+](C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 56, 56, 141, 141, 84, 141, 141, 201, 201, 201, 201, 141, 2, 2, 2, 1, 1, 1, 1, 7, 7, 141, 141, 95, 201, 201, 201, 201, 201, 201, 201, 201, 141] 201 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 34, 35] set([4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237081 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237081 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237081/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237081 Building REAL300000237082 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237082' /scratch/stefan/7769818/working/building/REAL300000237082 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237082 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237082/0 /scratch/stefan/7769818/working/building/REAL300000237082 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/82 `/scratch/stefan/7769818/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CN=C3C=CC(C(=O)[O-])=CN23)=C1) `REAL300000237082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237082 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CN=C3C=CC(C(=O)[O-])=CN23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', '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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 5, 5, 3, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 3, 5, 5, 3, 3, 1, 1, 1, 1, 5] 6 rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44]) total number of confs: 24 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237082 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CN=C3C=CC(C(=O)[O-])=CN23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', '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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1] 6 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 44, 36, 26, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237082 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237082 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237082/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237082 Building REAL300000237083 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237083' /scratch/stefan/7769818/working/building/REAL300000237083 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237083 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237083/0 /scratch/stefan/7769818/working/building/REAL300000237083 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/83 `/scratch/stefan/7769818/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(N3C=NC(C(=O)[O-])=C3)C=C2)=C1) `REAL300000237083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237083 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(N3C=NC(C(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', '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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 174, 178, 178, 79, 79, 36, 79, 79, 23, 3, 23, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 79, 178, 178, 178, 178, 178, 178, 174, 174, 37, 79, 79, 3, 3, 1, 1, 7, 7, 1, 1, 79] 201 rigid atoms, others: [47, 42, 43, 13, 14, 15, 16, 17, 18, 46, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 48]) total number of confs: 678 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237083 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(N3C=NC(C(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', '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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 127, 127, 81, 127, 127, 58, 11, 58, 11, 2, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 127, 201, 201, 201, 201, 201, 201, 201, 201, 80, 127, 127, 11, 11, 7, 7, 1, 1, 7, 7, 127] 201 rigid atoms, others: [44, 45, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 750 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: REAL300000237083 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(N3C=NC(C(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', '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, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 51, 51, 79, 79, 51, 51, 127, 127, 127, 127, 127, 127, 127, 79, 79, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 51, 51, 79, 79, 127, 127, 79, 79, 1] 201 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 39, 48, 38, 28, 5] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 407 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237083 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237083 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237083/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237083 Building REAL300000237084 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237084' /scratch/stefan/7769818/working/building/REAL300000237084 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237084 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237084/0 /scratch/stefan/7769818/working/building/REAL300000237084 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/84 `/scratch/stefan/7769818/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2F)=C1) `REAL300000237084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237084 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 194, 201, 201, 107, 107, 40, 107, 107, 39, 11, 39, 11, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 107, 201, 201, 201, 201, 201, 201, 194, 194, 51, 107, 107, 11, 11, 1, 1, 1, 107] 201 rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41]) total number of confs: 779 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237084 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 12, 12, 32, 32, 107, 107, 107, 107, 107, 154, 154, 107, 107, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 32, 32, 107, 107, 107, 1] 201 rigid atoms, others: [33, 34, 35, 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, 32, 36, 37, 38, 39, 40]) total number of confs: 403 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237084 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237084 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237084/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237084 Building REAL300000237085 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237085' /scratch/stefan/7769818/working/building/REAL300000237085 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237085 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237085/0 /scratch/stefan/7769818/working/building/REAL300000237085 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/85 `/scratch/stefan/7769818/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=C1) `REAL300000237085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237085 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 72, 80, 80, 29, 29, 13, 29, 29, 13, 5, 13, 5, 1, 1, 1, 1, 1, 1, 7, 14, 20, 20, 1, 1, 1, 29, 80, 80, 80, 80, 80, 80, 72, 72, 13, 29, 29, 5, 5, 1, 1, 14, 14, 1, 29] 201 rigid atoms, others: [40, 41, 44, 13, 14, 15, 16, 17, 18, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 45]) total number of confs: 404 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237085 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 29, 29, 29, 29, 103, 139, 142, 142, 29, 29, 29, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 9, 9, 29, 29, 139, 139, 29, 1] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 45, 36, 26, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 413 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237085 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237085 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237085/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237085 Building REAL300000237086 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237086' /scratch/stefan/7769818/working/building/REAL300000237086 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237086 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237086/0 /scratch/stefan/7769818/working/building/REAL300000237086 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/86 `/scratch/stefan/7769818/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=CC=C3C(=O)[O-])C=C2)=C1) `REAL300000237086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237086 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=CC=C3C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [116, 111, 116, 116, 50, 50, 26, 50, 50, 26, 4, 26, 4, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 9, 9, 1, 1, 50, 116, 116, 116, 116, 116, 116, 111, 111, 30, 50, 50, 4, 4, 1, 1, 7, 7, 6, 7, 1, 1, 50] 118 rigid atoms, others: [50, 49, 43, 44, 13, 14, 15, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 51]) total number of confs: 479 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237086 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=CC=C3C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 82, 82, 54, 82, 82, 54, 14, 54, 14, 6, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 82, 118, 118, 118, 118, 118, 118, 118, 118, 60, 82, 82, 14, 14, 7, 7, 1, 1, 1, 1, 7, 7, 82] 118 rigid atoms, others: [45, 46, 47, 48, 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, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51]) total number of confs: 478 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: REAL300000237086 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=CC=C(C3=CC=CC=C3C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 8, 8, 37, 37, 50, 50, 50, 50, 82, 82, 82, 82, 82, 82, 87, 87, 50, 50, 1, 9, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 37, 37, 50, 50, 82, 82, 82, 82, 50, 50, 1] 118 rigid atoms, others: [4, 5, 38, 7, 8, 9, 10, 39, 40, 51, 6, 29] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 225 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237086 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237086 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237086/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237086 Building REAL300000237087 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237087' /scratch/stefan/7769818/working/building/REAL300000237087 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237087 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237087/0 /scratch/stefan/7769818/working/building/REAL300000237087 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/87 `/scratch/stefan/7769818/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC=CC(C[NH+](C)C)=C1) `REAL300000237087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237087 none COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC=CC(C[NH+](C)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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 137, 137, 137, 137, 137, 137, 137, 137, 137, 42, 42, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 1, 156, 156, 156, 137, 137, 137, 42, 42, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 1] 201 rigid atoms, others: [34, 35, 36, 45, 13, 15, 16, 17, 18, 19, 20, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 299 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237087 none COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC=CC(C[NH+](C)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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 72, 72, 137, 137, 137, 137, 137, 195, 201, 201, 201, 137, 4, 4, 4, 1, 1, 1, 9, 9, 137, 137, 137, 195, 195, 201, 201, 201, 201, 201, 201, 137] 201 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, 42, 43, 44, 45]) total number of confs: 631 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237087 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237087 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237087/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237087 Building REAL300000237088 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237088' /scratch/stefan/7769818/working/building/REAL300000237088 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237088 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237088/0 /scratch/stefan/7769818/working/building/REAL300000237088 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/88 `/scratch/stefan/7769818/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=CC(C(=O)C=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)=C1) `REAL300000237088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237088 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 9, 9, 5, 9, 9, 5, 3, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 10, 10, 10, 10, 10, 5, 9, 9, 3, 3, 1, 1, 1, 9] 10 rigid atoms, others: [41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237088 none C[NH+](C)CC1=CC=CC(C(=O)C=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 5, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 8, 8, 9, 9, 9, 1] 10 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 44, 38, 4, 27, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237088 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237088 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237088/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237088 Building REAL300000237089 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237089' /scratch/stefan/7769818/working/building/REAL300000237089 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237089 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237089/0 /scratch/stefan/7769818/working/building/REAL300000237089 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/89 `/scratch/stefan/7769818/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(OCC(=O)[O-])C(OC)=C2)=C1) `REAL300000237089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237089 none COC1=NOC(C(=O)C=CC2=CC=C(OCC(=O)[O-])C(OC)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', '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, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 42, 42, 24, 5, 24, 5, 1, 1, 1, 1, 1, 1, 9, 42, 67, 67, 1, 1, 3, 1, 42, 46, 46, 46, 5, 5, 1, 1, 42, 42, 3, 3, 3, 1, 42] 201 rigid atoms, others: [36, 9, 10, 11, 12, 13, 14, 19, 20, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 37]) total number of confs: 315 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237089 none COC1=NOC(C(=O)C=CC2=CC=C(OCC(=O)[O-])C(OC)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', '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, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 16, 17, 42, 42, 42, 41, 101, 185, 197, 197, 42, 42, 57, 42, 1, 2, 2, 2, 17, 16, 42, 42, 185, 185, 57, 57, 57, 42, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 23, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 634 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237089 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237089 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237089/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237089 Building REAL300000237090 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237090' /scratch/stefan/7769818/working/building/REAL300000237090 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237090 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237090/0 /scratch/stefan/7769818/working/building/REAL300000237090 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/90 `/scratch/stefan/7769818/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(OCC(=O)[O-])C=C2)=C1) `REAL300000237090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237090 none COC1=NOC(C(=O)C=CC2=CC=C(OCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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: [56, 46, 46, 46, 46, 17, 3, 17, 3, 1, 1, 1, 1, 1, 1, 6, 24, 42, 42, 1, 1, 46, 56, 56, 56, 3, 3, 1, 1, 24, 24, 1, 1, 46] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 19, 20, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 33]) total number of confs: 230 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237090 none COC1=NOC(C(=O)C=CC2=CC=C(OCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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: [2, 1, 1, 1, 1, 1, 1, 9, 9, 31, 31, 46, 46, 31, 31, 116, 199, 201, 201, 46, 46, 1, 2, 2, 2, 31, 31, 46, 46, 199, 199, 46, 46, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 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]) total number of confs: 676 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237090 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237090 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237090/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237090 Building REAL300000237091 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237091' /scratch/stefan/7769818/working/building/REAL300000237091 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237091 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237091/0 /scratch/stefan/7769818/working/building/REAL300000237091 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/91 `/scratch/stefan/7769818/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(OCCC(=O)[O-])C=C2)=C1) `REAL300000237091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237091 none COC1=NOC(C(=O)C=CC2=CC=C(OCCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 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, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 42, 42, 42, 42, 18, 3, 18, 3, 1, 1, 1, 1, 1, 1, 6, 27, 41, 61, 50, 1, 1, 42, 48, 48, 48, 3, 3, 1, 1, 27, 27, 41, 41, 1, 1, 42] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 36]) total number of confs: 299 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237091 none COC1=NOC(C(=O)C=CC2=CC=C(OCCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 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, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 29, 29, 42, 42, 29, 29, 115, 175, 187, 201, 188, 42, 42, 1, 2, 2, 2, 29, 29, 42, 42, 175, 175, 187, 187, 42, 42, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 22, 36] set([0, 7, 8, 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, 35]) total number of confs: 654 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237091 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237091 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237091/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237091 Building REAL300000237092 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237092' /scratch/stefan/7769818/working/building/REAL300000237092 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237092 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237092/0 /scratch/stefan/7769818/working/building/REAL300000237092 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/92 `/scratch/stefan/7769818/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=CC(OC(C)C(=O)[O-])=C2)=C1) `REAL300000237092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237092 none COC1=NOC(C(=O)C=CC2=CC=CC(OC(C)C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 46, 46, 46, 46, 22, 6, 21, 6, 1, 1, 1, 1, 1, 1, 1, 11, 28, 28, 42, 42, 1, 46, 55, 55, 55, 6, 6, 1, 1, 1, 28, 28, 28, 28, 1, 46] 201 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 36]) total number of confs: 243 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237092 none COC1=NOC(C(=O)C=CC2=CC=CC(OC(C)C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 26, 26, 46, 46, 45, 46, 46, 123, 194, 194, 199, 199, 46, 1, 3, 3, 3, 26, 26, 46, 46, 45, 194, 194, 194, 194, 46, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 22, 36] set([0, 7, 8, 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, 35]) total number of confs: 583 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237092 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237092 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237092/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237092 Building REAL300000237093 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237093' /scratch/stefan/7769818/working/building/REAL300000237093 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237093 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237093/0 /scratch/stefan/7769818/working/building/REAL300000237093 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/93 `/scratch/stefan/7769818/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=CC(OCCC(=O)[O-])=C2)=C1) `REAL300000237093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237093 none COC1=NOC(C(=O)C=CC2=CC=CC(OCCC(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 48, 48, 48, 48, 30, 6, 29, 6, 1, 1, 1, 1, 1, 1, 1, 6, 19, 27, 38, 34, 1, 48, 56, 56, 56, 6, 6, 1, 1, 1, 19, 19, 27, 27, 1, 48] 201 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 36]) total number of confs: 251 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237093 none COC1=NOC(C(=O)C=CC2=CC=CC(OCCC(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 18, 18, 48, 48, 48, 48, 48, 127, 163, 181, 201, 199, 48, 1, 2, 2, 2, 18, 18, 48, 48, 48, 163, 163, 181, 181, 48, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 22, 36] set([0, 7, 8, 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, 35]) total number of confs: 553 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237093 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237093 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237093/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237093 Building REAL300000237094 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237094' /scratch/stefan/7769818/working/building/REAL300000237094 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237094 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237094/0 /scratch/stefan/7769818/working/building/REAL300000237094 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/94 `/scratch/stefan/7769818/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=C1) `REAL300000237094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237094 none COC1=NOC(C(=O)C=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 71, 71, 71, 71, 32, 7, 31, 7, 1, 1, 1, 1, 1, 1, 1, 2, 6, 18, 18, 17, 18, 18, 18, 23, 23, 1, 71, 78, 78, 78, 7, 7, 1, 1, 1, 6, 6, 18, 18, 17, 18, 1, 71] 201 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 43]) total number of confs: 198 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237094 none COC1=NOC(C(=O)C=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 194, 194, 194, 194, 140, 53, 140, 53, 18, 18, 18, 18, 18, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 18, 194, 201, 201, 201, 53, 53, 18, 17, 18, 6, 6, 1, 1, 1, 1, 18, 194] 201 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 473 number of broken/clashed sets: 23 ./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: REAL300000237094 none COC1=NOC(C(=O)C=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 26, 26, 71, 71, 70, 71, 71, 101, 108, 194, 194, 194, 194, 194, 194, 201, 201, 71, 1, 3, 3, 3, 26, 26, 71, 71, 70, 108, 108, 194, 194, 194, 194, 71, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 43, 27] set([0, 7, 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, 38, 39, 40, 41, 42]) total number of confs: 394 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237094 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237094 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237094/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237094 Building REAL300000237095 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237095' /scratch/stefan/7769818/working/building/REAL300000237095 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237095 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237095/0 /scratch/stefan/7769818/working/building/REAL300000237095 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/95 `/scratch/stefan/7769818/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)=C1) `REAL300000237095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237095 none COC1=NOC(C(=O)C=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 39, 39, 39, 39, 16, 3, 16, 3, 1, 1, 1, 1, 1, 1, 2, 10, 29, 29, 29, 29, 29, 43, 43, 29, 1, 1, 39, 45, 45, 45, 3, 3, 1, 1, 10, 10, 29, 29, 29, 29, 1, 1, 39] 201 rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 14, 41, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 191 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237095 none COC1=NOC(C(=O)C=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 177, 177, 177, 177, 140, 51, 140, 51, 29, 28, 29, 29, 17, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 29, 29, 177, 201, 201, 201, 51, 51, 28, 29, 9, 9, 1, 2, 2, 2, 29, 29, 177] 201 rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 515 number of broken/clashed sets: 19 ./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: REAL300000237095 none COC1=NOC(C(=O)C=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 9, 9, 29, 29, 39, 39, 29, 29, 60, 75, 177, 177, 177, 177, 177, 201, 201, 177, 39, 39, 1, 3, 3, 3, 29, 28, 39, 39, 75, 75, 177, 177, 177, 177, 39, 39, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 43, 27] set([0, 7, 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, 38, 39, 40, 41, 42]) total number of confs: 469 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237095 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237095 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237095/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237095 Building REAL300000237096 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237096' /scratch/stefan/7769818/working/building/REAL300000237096 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237096 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237096/0 /scratch/stefan/7769818/working/building/REAL300000237096 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/96 `/scratch/stefan/7769818/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)=C1) `REAL300000237096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237096 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [88, 77, 77, 77, 77, 40, 12, 39, 12, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 6, 6, 7, 7, 1, 77, 88, 88, 88, 13, 12, 1, 1, 7, 7, 7, 7, 76] 140 rigid atoms, others: [9, 10, 11, 12, 13, 14, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 207 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237096 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 140, 140, 140, 96, 53, 96, 53, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 140, 140, 140, 140, 53, 53, 7, 7, 1, 1, 1, 1, 140] 140 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 310 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: REAL300000237096 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 10, 10, 37, 38, 76, 77, 77, 77, 140, 140, 77, 77, 140, 140, 140, 140, 77, 1, 3, 3, 3, 37, 37, 76, 77, 140, 140, 140, 140, 1] 140 rigid atoms, others: [1, 2, 3, 4, 5, 6, 24, 36] set([0, 7, 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, 35]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237096 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237096 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237096/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237096 Building REAL300000237097 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237097' /scratch/stefan/7769818/working/building/REAL300000237097 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237097 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237097/0 /scratch/stefan/7769818/working/building/REAL300000237097 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/97 `/scratch/stefan/7769818/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=C1) `REAL300000237097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237097 none COC1=NOC(C(=O)C=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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: [40, 39, 39, 39, 39, 25, 5, 25, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 16, 16, 16, 16, 17, 17, 17, 16, 1, 39, 40, 40, 40, 5, 5, 1, 1, 1, 2, 2, 16, 16, 16, 16, 1, 39] 201 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 43]) total number of confs: 105 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237097 none COC1=NOC(C(=O)C=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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, 201, 201, 201, 161, 65, 161, 65, 16, 16, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 16, 201, 201, 201, 201, 65, 65, 16, 17, 16, 8, 8, 1, 1, 1, 1, 16, 201] 201 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 539 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: REAL300000237097 none COC1=NOC(C(=O)C=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 39, 39, 39, 39, 39, 61, 61, 201, 201, 201, 201, 201, 201, 201, 201, 39, 1, 2, 2, 2, 18, 18, 39, 39, 39, 61, 61, 201, 201, 201, 201, 39, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 43, 27] set([0, 7, 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, 38, 39, 40, 41, 42]) total number of confs: 307 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237097 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237097 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237097/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237097 Building REAL300000237098 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237098' /scratch/stefan/7769818/working/building/REAL300000237098 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237098 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237098/0 /scratch/stefan/7769818/working/building/REAL300000237098 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/98 `/scratch/stefan/7769818/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC(OC)=C(OCC(=O)[O-])C=C2[N+](=O)[O-])=C1) `REAL300000237098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237098 none COC1=NOC(C(=O)C=CC2=CC(OC)=C(OCC(=O)[O-])C=C2[N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 49, 49, 49, 49, 27, 5, 27, 5, 1, 1, 1, 1, 1, 3, 1, 1, 9, 21, 32, 32, 1, 1, 1, 2, 2, 49, 57, 57, 57, 5, 5, 1, 4, 4, 4, 21, 21, 1, 49] 201 rigid atoms, others: [32, 38, 9, 10, 11, 12, 13, 15, 16, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 39]) total number of confs: 229 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237098 none COC1=NOC(C(=O)C=CC2=CC(OC)=C(OCC(=O)[O-])C=C2[N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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 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, 20, 20, 49, 49, 49, 85, 49, 49, 144, 193, 193, 193, 49, 49, 49, 49, 49, 1, 3, 3, 3, 20, 20, 49, 85, 85, 85, 193, 193, 49, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 26] set([0, 7, 8, 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: 547 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237098 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237098 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237098/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237098 Building REAL300000237099 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237099' /scratch/stefan/7769818/working/building/REAL300000237099 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237099 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237099/0 /scratch/stefan/7769818/working/building/REAL300000237099 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/99 `/scratch/stefan/7769818/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=CC(OCC(=O)[O-])=C2)=C1) `REAL300000237099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237099 none COC1=NOC(C(=O)C=CC2=CC=CC(OCC(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 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, 3, 7, 7, 3, 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] 0 hydrogens 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, 51, 51, 51, 51, 28, 6, 27, 6, 1, 1, 1, 1, 1, 1, 1, 5, 21, 33, 33, 1, 51, 59, 59, 59, 6, 6, 1, 1, 1, 21, 21, 1, 51] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30, 31, 33]) total number of confs: 227 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237099 none COC1=NOC(C(=O)C=CC2=CC=CC(OCC(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 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, 3, 7, 7, 3, 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] 0 hydrogens 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, 6, 6, 24, 24, 51, 51, 51, 51, 51, 115, 186, 201, 201, 51, 1, 3, 3, 3, 24, 24, 51, 51, 51, 186, 186, 51, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 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]) total number of confs: 622 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237099 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237099 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237099/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237099 Building REAL300000237100 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237100' /scratch/stefan/7769818/working/building/REAL300000237100 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237100 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237100/0 /scratch/stefan/7769818/working/building/REAL300000237100 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/100 `/scratch/stefan/7769818/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)=C1) `REAL300000237100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237100 none COC1=NOC(C(=O)C=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [41, 32, 32, 32, 32, 16, 4, 15, 4, 1, 1, 1, 1, 1, 1, 2, 10, 26, 26, 32, 32, 26, 26, 26, 1, 1, 32, 41, 41, 41, 4, 4, 1, 1, 10, 10, 26, 26, 1, 1, 32] 135 rigid atoms, others: [32, 33, 38, 39, 9, 10, 11, 12, 13, 14, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 40]) total number of confs: 159 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237100 none COC1=NOC(C(=O)C=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 126, 126, 126, 126, 98, 45, 98, 45, 26, 25, 26, 26, 14, 6, 1, 1, 1, 1, 3, 3, 1, 1, 1, 26, 26, 126, 135, 135, 135, 45, 45, 25, 26, 6, 6, 1, 1, 26, 26, 126] 135 rigid atoms, others: [36, 37, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 347 number of broken/clashed sets: 27 ./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: REAL300000237100 none COC1=NOC(C(=O)C=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 9, 9, 25, 25, 32, 32, 25, 25, 54, 71, 126, 126, 135, 135, 126, 126, 126, 32, 32, 1, 2, 2, 2, 25, 24, 32, 32, 71, 71, 126, 126, 32, 32, 1] 135 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 26] set([0, 7, 8, 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, 39]) total number of confs: 345 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237100 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237100 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237100/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237100 Building REAL300000237101 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237101' /scratch/stefan/7769818/working/building/REAL300000237101 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237101 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237101/0 /scratch/stefan/7769818/working/building/REAL300000237101 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/101 `/scratch/stefan/7769818/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=C1) `REAL300000237101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237101 none COC1=NOC(C(=O)C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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] 0 hydrogens 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, 34, 34, 34, 34, 15, 3, 15, 3, 1, 1, 1, 1, 1, 1, 12, 48, 48, 48, 77, 77, 1, 1, 34, 38, 38, 38, 3, 3, 1, 1, 1, 1, 34] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 33]) total number of confs: 332 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237101 none COC1=NOC(C(=O)C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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] 0 hydrogens 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, 7, 7, 23, 23, 34, 34, 23, 23, 123, 185, 185, 185, 201, 201, 34, 34, 1, 3, 3, 3, 23, 23, 34, 34, 34, 34, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 23] set([0, 7, 8, 9, 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: 596 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237101 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237101 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237101/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237101 Building REAL300000237102 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237102' /scratch/stefan/7769818/working/building/REAL300000237102 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237102 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237102/0 /scratch/stefan/7769818/working/building/REAL300000237102 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/102 `/scratch/stefan/7769818/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)=C1) `REAL300000237102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237102 none COC1=NOC(C(=O)C=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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: [72, 63, 63, 63, 63, 34, 5, 34, 5, 1, 1, 1, 1, 1, 1, 7, 30, 51, 51, 1, 1, 1, 63, 72, 72, 72, 5, 5, 1, 1, 30, 30, 1, 63] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 30, 31, 33]) total number of confs: 298 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237102 none COC1=NOC(C(=O)C=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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: [2, 1, 1, 1, 1, 1, 1, 8, 8, 25, 25, 63, 63, 63, 63, 137, 197, 201, 201, 63, 63, 63, 1, 2, 2, 2, 25, 25, 63, 63, 197, 197, 63, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 22] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 515 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237102 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237102 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237102/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237102 Building REAL300000237103 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237103' /scratch/stefan/7769818/working/building/REAL300000237103 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237103 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237103/0 /scratch/stefan/7769818/working/building/REAL300000237103 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/103 `/scratch/stefan/7769818/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=C3C=C(C(=O)[O-])OC3=C(OC)C=C2)=C1) `REAL300000237103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237103 none COC1=NOC(C(=O)C=CC2=C3C=C(C(=O)[O-])OC3=C(OC)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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: [201, 158, 158, 158, 158, 65, 11, 65, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 158, 201, 201, 201, 11, 11, 1, 3, 3, 3, 1, 1, 157] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 36, 33, 21, 24, 25, 26, 27, 28, 29, 31]) total number of confs: 365 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237103 none COC1=NOC(C(=O)C=CC2=C3C=C(C(=O)[O-])OC3=C(OC)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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: [3, 1, 1, 1, 1, 1, 1, 12, 12, 57, 58, 158, 158, 158, 158, 158, 158, 158, 158, 157, 158, 201, 158, 158, 1, 3, 3, 3, 58, 57, 158, 201, 201, 201, 158, 158, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 24, 36] set([0, 7, 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, 35]) total number of confs: 370 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237103 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237103 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237103/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237103 Building REAL300000237104 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237104' /scratch/stefan/7769818/working/building/REAL300000237104 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237104 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237104/0 /scratch/stefan/7769818/working/building/REAL300000237104 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/104 `/scratch/stefan/7769818/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(OCCC(=O)[O-])C(OC)=C2)=C1) `REAL300000237104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237104 none COC1=NOC(C(=O)C=CC2=CC=C(OCCC(=O)[O-])C(OC)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 40, 40, 40, 40, 22, 5, 22, 5, 1, 1, 1, 1, 1, 1, 9, 35, 35, 55, 49, 1, 1, 3, 1, 40, 44, 44, 44, 5, 5, 1, 1, 35, 35, 35, 35, 3, 3, 3, 1, 40] 201 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 20, 21, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 273 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237104 none COC1=NOC(C(=O)C=CC2=CC=C(OCCC(=O)[O-])C(OC)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 15, 16, 40, 40, 40, 39, 125, 186, 186, 201, 199, 40, 40, 70, 40, 1, 3, 3, 3, 16, 15, 40, 40, 186, 186, 186, 186, 70, 70, 70, 40, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 24] set([0, 7, 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, 35, 36, 37, 38, 39]) total number of confs: 604 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237104 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237104 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237104/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237104 Building REAL300000237105 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237105' /scratch/stefan/7769818/working/building/REAL300000237105 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237105 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237105/0 /scratch/stefan/7769818/working/building/REAL300000237105 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/105 `/scratch/stefan/7769818/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2Cl)=C1) `REAL300000237105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237105 none COC1=NOC(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 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 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 68, 68, 68, 68, 42, 9, 42, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 68, 77, 77, 77, 9, 9, 1, 1, 1, 68] 77 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 163 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237105 none COC1=NOC(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 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 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, 10, 10, 38, 39, 68, 68, 52, 61, 68, 68, 68, 68, 68, 1, 3, 3, 3, 38, 38, 68, 68, 68, 1] 77 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 232 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237105 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237105 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237105/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237105 Building REAL300000237106 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237106' /scratch/stefan/7769818/working/building/REAL300000237106 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237106 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237106/0 /scratch/stefan/7769818/working/building/REAL300000237106 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/106 `/scratch/stefan/7769818/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2Cl)=C1) `REAL300000237106.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237106 none COC1=NOC(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [130, 115, 115, 115, 115, 59, 9, 59, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 115, 130, 130, 130, 9, 9, 1, 1, 1, 115] 130 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 258 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237106 none COC1=NOC(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 12, 12, 58, 58, 115, 115, 115, 115, 115, 128, 128, 115, 115, 1, 3, 3, 3, 58, 58, 115, 115, 115, 1] 130 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 281 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237106 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237106 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237106/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237106 Building REAL300000237107 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237107' /scratch/stefan/7769818/working/building/REAL300000237107 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237107 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237107/0 /scratch/stefan/7769818/working/building/REAL300000237107 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/107 `/scratch/stefan/7769818/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC(C(=O)[O-])=C(C)C=C2C)=C1) `REAL300000237107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237107 none COC1=NOC(C(=O)C=CC2=CC(C(=O)[O-])=C(C)C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [170, 143, 143, 143, 143, 63, 9, 63, 9, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 143, 170, 170, 170, 9, 9, 1, 2, 2, 2, 1, 2, 2, 2, 143] 170 rigid atoms, others: [9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 27, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 329 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237107 none COC1=NOC(C(=O)C=CC2=CC(C(=O)[O-])=C(C)C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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, 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: [2, 1, 1, 1, 1, 1, 1, 13, 13, 64, 64, 143, 143, 143, 169, 169, 143, 143, 143, 143, 143, 1, 3, 3, 3, 64, 64, 143, 143, 143, 143, 143, 143, 143, 143, 1] 170 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 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, 34]) total number of confs: 383 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237107 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237107 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237107/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237107 Building REAL300000237108 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237108' /scratch/stefan/7769818/working/building/REAL300000237108 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237108 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237108/0 /scratch/stefan/7769818/working/building/REAL300000237108 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/108 `/scratch/stefan/7769818/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(OC(C)C(=O)[O-])C=C2)=C1) `REAL300000237108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237108 none COC1=NOC(C(=O)C=CC2=CC=C(OC(C)C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 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, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 42, 42, 42, 42, 17, 3, 17, 3, 1, 1, 1, 1, 1, 1, 11, 30, 30, 42, 42, 1, 1, 42, 51, 51, 51, 3, 3, 1, 1, 30, 30, 30, 30, 1, 1, 42] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 36]) total number of confs: 233 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237108 none COC1=NOC(C(=O)C=CC2=CC=C(OC(C)C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 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, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 27, 27, 42, 42, 27, 28, 137, 190, 190, 201, 201, 42, 42, 1, 2, 2, 2, 27, 27, 42, 42, 190, 190, 190, 190, 42, 42, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 22, 36] set([0, 7, 8, 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, 35]) total number of confs: 596 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237108 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237108 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237108/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237108 Building REAL300000237109 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237109' /scratch/stefan/7769818/working/building/REAL300000237109 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237109 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237109/0 /scratch/stefan/7769818/working/building/REAL300000237109 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/109 `/scratch/stefan/7769818/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=CC=C2OCCC(=O)[O-])=C1) `REAL300000237109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237109 none COC1=NOC(C(=O)C=CC2=CC=CC=C2OCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 58, 58, 58, 58, 24, 9, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 33, 59, 55, 58, 64, 64, 64, 9, 9, 1, 1, 1, 1, 27, 27, 33, 33, 58] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) total number of confs: 328 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237109 none COC1=NOC(C(=O)C=CC2=CC=CC=C2OCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 25, 25, 58, 58, 30, 58, 58, 58, 132, 192, 194, 201, 191, 1, 2, 2, 2, 25, 25, 58, 58, 58, 58, 192, 192, 194, 194, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 22, 36] set([0, 7, 8, 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, 35]) total number of confs: 667 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237109 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237109 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237109/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237109 Building REAL300000237110 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237110' /scratch/stefan/7769818/working/building/REAL300000237110 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237110 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237110/0 /scratch/stefan/7769818/working/building/REAL300000237110 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/110 `/scratch/stefan/7769818/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=C1) `REAL300000237110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237110 none COC1=NOC(C(=O)C=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 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, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 30, 16, 6, 15, 6, 1, 1, 1, 1, 1, 1, 1, 12, 33, 43, 43, 33, 48, 48, 33, 48, 48, 1, 30, 31, 31, 31, 6, 6, 1, 1, 1, 33, 48, 48, 33, 48, 48, 1, 30] 201 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 43]) total number of confs: 285 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237110 none COC1=NOC(C(=O)C=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 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, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 200, 200, 200, 191, 136, 191, 136, 48, 48, 48, 48, 48, 9, 3, 1, 3, 4, 4, 1, 1, 1, 1, 1, 1, 48, 200, 201, 201, 201, 136, 136, 48, 48, 48, 3, 1, 1, 1, 1, 1, 48, 200] 201 rigid atoms, others: [37, 38, 39, 40, 41, 16, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43]) total number of confs: 543 number of broken/clashed sets: 7 ./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: REAL300000237110 none COC1=NOC(C(=O)C=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 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, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 12, 12, 30, 30, 29, 30, 30, 107, 197, 200, 200, 197, 200, 200, 197, 200, 200, 30, 1, 3, 3, 3, 12, 12, 30, 30, 29, 197, 200, 200, 197, 200, 200, 30, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 43, 27] set([0, 7, 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, 38, 39, 40, 41, 42]) total number of confs: 615 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237110 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237110 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237110/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237110 Building REAL300000237111 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237111' /scratch/stefan/7769818/working/building/REAL300000237111 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237111 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237111/0 /scratch/stefan/7769818/working/building/REAL300000237111 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/111 `/scratch/stefan/7769818/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(OC)C(C(=O)[O-])=C2)=C1) `REAL300000237111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237111 none COC1=NOC(C(=O)C=CC2=CC=C(OC)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 112, 112, 112, 112, 39, 6, 39, 6, 1, 1, 1, 1, 1, 1, 3, 1, 1, 3, 3, 1, 112, 137, 137, 137, 6, 6, 1, 1, 3, 3, 3, 1, 112] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 16, 17, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33]) total number of confs: 245 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237111 none COC1=NOC(C(=O)C=CC2=CC=C(OC)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 53, 53, 112, 112, 112, 112, 167, 112, 112, 160, 160, 112, 1, 2, 2, 2, 53, 53, 112, 112, 167, 167, 167, 112, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 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]) total number of confs: 524 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237111 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237111 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237111/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237111 Building REAL300000237112 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237112' /scratch/stefan/7769818/working/building/REAL300000237112 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237112 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237112/0 /scratch/stefan/7769818/working/building/REAL300000237112 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/112 `/scratch/stefan/7769818/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC(C(=O)[O-])=C(OC)C=C2OC)=C1) `REAL300000237112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237112 none COC1=NOC(C(=O)C=CC2=CC(C(=O)[O-])=C(OC)C=C2OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 87, 87, 87, 87, 55, 9, 55, 9, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 1, 1, 1, 3, 87, 98, 98, 98, 9, 9, 1, 4, 4, 4, 1, 4, 4, 4, 87] 201 rigid atoms, others: [33, 9, 10, 11, 12, 13, 16, 17, 19, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 223 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237112 none COC1=NOC(C(=O)C=CC2=CC(C(=O)[O-])=C(OC)C=C2OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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 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, 8, 28, 29, 87, 87, 87, 121, 121, 87, 87, 132, 87, 87, 87, 131, 1, 3, 3, 3, 29, 28, 87, 132, 132, 132, 87, 131, 131, 131, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 23, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 457 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237112 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237112 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237112/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237112 Building REAL300000237113 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237113' /scratch/stefan/7769818/working/building/REAL300000237113 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237113 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237113/0 /scratch/stefan/7769818/working/building/REAL300000237113 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/113 `/scratch/stefan/7769818/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC(Br)=CC(C(=O)[O-])=C2)=C1) `REAL300000237113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237113 none COC1=NOC(C(=O)C=CC2=CC(Br)=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 78, 78, 78, 78, 37, 5, 37, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 96, 96, 96, 5, 5, 1, 1, 1, 78] 96 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 184 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237113 none COC1=NOC(C(=O)C=CC2=CC(Br)=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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] 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, 12, 12, 37, 37, 78, 78, 78, 78, 78, 78, 78, 78, 78, 1, 3, 3, 3, 37, 36, 78, 78, 78, 1] 96 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237113 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237113 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237113/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237113 Building REAL300000237114 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237114' /scratch/stefan/7769818/working/building/REAL300000237114 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237114 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237114/0 /scratch/stefan/7769818/working/building/REAL300000237114 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/114 `/scratch/stefan/7769818/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC(F)=C(C(=O)[O-])C=C2F)=C1) `REAL300000237114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237114 none COC1=NOC(C(=O)C=CC2=CC(F)=C(C(=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [185, 142, 142, 142, 142, 71, 11, 71, 11, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 142, 185, 185, 185, 11, 11, 1, 1, 142] 185 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 363 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237114 none COC1=NOC(C(=O)C=CC2=CC(F)=C(C(=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 12, 12, 54, 55, 142, 142, 142, 141, 142, 172, 172, 142, 142, 142, 1, 3, 3, 3, 55, 54, 142, 142, 1] 185 rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 378 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237114 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237114 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237114/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237114 Building REAL300000237115 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237115' /scratch/stefan/7769818/working/building/REAL300000237115 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237115 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237115/0 /scratch/stefan/7769818/working/building/REAL300000237115 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/115 `/scratch/stefan/7769818/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=C3C(=CC=C2)NN=C3C(=O)[O-])=C1) `REAL300000237115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237115 none COC1=NOC(C(=O)C=CC2=C3C(=CC=C2)NN=C3C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', '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, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 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, 131, 131, 131, 131, 61, 9, 61, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 131, 138, 138, 138, 9, 9, 1, 1, 1, 1, 131] 138 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 261 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237115 none COC1=NOC(C(=O)C=CC2=C3C(=CC=C2)NN=C3C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', '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, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 12, 12, 70, 71, 131, 131, 131, 131, 131, 131, 131, 131, 131, 138, 138, 1, 3, 3, 3, 70, 70, 131, 131, 131, 131, 1] 138 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 22] set([0, 7, 8, 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: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237115 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237115 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237115/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237115 Building REAL300000237116 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237116' /scratch/stefan/7769818/working/building/REAL300000237116 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237116 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237116/0 /scratch/stefan/7769818/working/building/REAL300000237116 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/116 `/scratch/stefan/7769818/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)=C1) `REAL300000237116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237116 none COC1=NOC(C(=O)C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 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, 3, 7, 7, 3, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 92, 92, 92, 92, 43, 11, 43, 11, 1, 1, 1, 1, 1, 6, 14, 14, 1, 1, 1, 6, 6, 2, 6, 6, 92, 103, 103, 103, 11, 11, 1, 6, 6, 6, 6, 5, 6, 6, 92] 201 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237116 none COC1=NOC(C(=O)C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 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, 3, 7, 7, 3, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [149, 132, 132, 132, 132, 79, 32, 79, 32, 6, 6, 6, 6, 6, 24, 39, 39, 6, 1, 1, 1, 1, 1, 1, 1, 132, 149, 149, 149, 32, 32, 6, 24, 24, 1, 1, 1, 1, 1, 132] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39]) 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: REAL300000237116 none COC1=NOC(C(=O)C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 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, 3, 7, 7, 3, 7, 7, 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 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, 8, 8, 24, 24, 92, 92, 92, 181, 185, 185, 92, 84, 92, 132, 132, 120, 132, 132, 1, 3, 3, 3, 24, 24, 92, 181, 181, 132, 132, 132, 132, 132, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 754 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237116 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237116 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237116/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237116 Building REAL300000237117 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237117' /scratch/stefan/7769818/working/building/REAL300000237117 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237117 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237117/0 /scratch/stefan/7769818/working/building/REAL300000237117 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/117 `/scratch/stefan/7769818/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CN(CC(=O)[O-])N=C2C2=CC=C(OC)C=C2)=C1) `REAL300000237117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237117 none COC1=NOC(C(=O)C=CC2=CN(CC(=O)[O-])N=C2C2=CC=C(OC)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 65, 65, 65, 65, 40, 12, 39, 12, 1, 1, 1, 1, 1, 6, 10, 10, 1, 1, 1, 6, 6, 1, 1, 11, 6, 6, 65, 68, 68, 68, 12, 12, 1, 6, 6, 6, 6, 11, 11, 11, 6, 6, 65] 201 rigid atoms, others: [33, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237117 none COC1=NOC(C(=O)C=CC2=CN(CC(=O)[O-])N=C2C2=CC=C(OC)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 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] 0 hydrogens 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, 106, 106, 106, 106, 69, 31, 69, 31, 6, 6, 6, 6, 6, 22, 30, 30, 6, 1, 1, 1, 1, 1, 1, 2, 1, 1, 106, 112, 112, 112, 31, 31, 6, 22, 22, 1, 1, 3, 3, 3, 1, 1, 106] 201 rigid atoms, others: [36, 37, 41, 42, 18, 19, 20, 21, 22, 23, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 43]) total number of confs: 354 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: REAL300000237117 none COC1=NOC(C(=O)C=CC2=CN(CC(=O)[O-])N=C2C2=CC=C(OC)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 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] 0 hydrogens 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, 6, 6, 20, 21, 65, 65, 65, 138, 146, 146, 65, 57, 65, 106, 106, 65, 65, 144, 106, 106, 1, 3, 3, 3, 20, 20, 65, 138, 138, 106, 106, 144, 144, 144, 106, 106, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 43, 27] set([0, 7, 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, 38, 39, 40, 41, 42]) total number of confs: 802 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237117 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237117 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237117/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237117 Building REAL300000237118 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237118' /scratch/stefan/7769818/working/building/REAL300000237118 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237118 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237118/0 /scratch/stefan/7769818/working/building/REAL300000237118 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/118 `/scratch/stefan/7769818/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C(O)=C3)O2)=C1) `REAL300000237118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237118 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C(O)=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 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: [77, 66, 66, 66, 66, 32, 12, 31, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 21, 21, 12, 12, 12, 1, 66, 77, 77, 77, 13, 12, 1, 1, 12, 12, 24, 12, 65] 402 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 221 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237118 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C(O)=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 142, 77, 141, 76, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 12, 201, 201, 201, 201, 77, 76, 12, 12, 1, 1, 2, 1, 200] 402 rigid atoms, others: [33, 34, 36, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 37]) total number of confs: 450 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: REAL300000237118 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C(O)=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 8, 8, 37, 38, 65, 66, 66, 66, 201, 201, 201, 201, 201, 201, 201, 201, 201, 66, 1, 3, 3, 3, 37, 37, 65, 66, 201, 201, 402, 201, 1] 402 rigid atoms, others: [1, 2, 3, 4, 5, 6, 25, 37] set([0, 7, 8, 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]) total number of confs: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237118 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237118 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237118/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237118 Building REAL300000237119 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237119' /scratch/stefan/7769818/working/building/REAL300000237119 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237119 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237119/0 /scratch/stefan/7769818/working/building/REAL300000237119 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/119 `/scratch/stefan/7769818/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)=C1) `REAL300000237119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237119 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', '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', '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, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [51, 48, 48, 48, 48, 22, 3, 22, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 3, 1, 1, 48, 51, 51, 51, 3, 3, 1, 1, 3, 3, 3, 3, 1, 1, 48] 59 rigid atoms, others: [32, 37, 38, 9, 10, 11, 12, 13, 14, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39]) total number of confs: 106 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237119 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', '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', '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, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 33, 5, 33, 5, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 59, 59, 59, 59, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 59] 59 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 128 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: REAL300000237119 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', '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', '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, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 13, 13, 40, 40, 48, 48, 40, 40, 59, 59, 40, 41, 59, 59, 59, 59, 48, 48, 1, 3, 3, 3, 40, 40, 48, 48, 59, 59, 59, 59, 48, 48, 1] 59 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 297 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237119 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237119 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237119/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237119 Building REAL300000237120 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237120' /scratch/stefan/7769818/working/building/REAL300000237120 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237120 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237120/0 /scratch/stefan/7769818/working/building/REAL300000237120 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/120 `/scratch/stefan/7769818/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CNC3=CC=C(C(=O)[O-])C=C23)=C1) `REAL300000237120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237120 none COC1=NOC(C(=O)C=CC2=CNC3=CC=C(C(=O)[O-])C=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 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 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 152, 152, 152, 152, 73, 12, 72, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 152, 158, 158, 158, 12, 12, 1, 1, 1, 1, 1, 152] 158 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 33, 18, 19, 22, 23, 24, 25, 26, 27]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237120 none COC1=NOC(C(=O)C=CC2=CNC3=CC=C(C(=O)[O-])C=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 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 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 12, 12, 55, 55, 152, 152, 152, 152, 152, 152, 152, 152, 152, 152, 152, 1, 3, 3, 3, 55, 55, 152, 152, 152, 152, 152, 1] 158 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 22] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237120 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237120 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237120/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237120 Building REAL300000237121 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237121' /scratch/stefan/7769818/working/building/REAL300000237121 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237121 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237121/0 /scratch/stefan/7769818/working/building/REAL300000237121 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/121 `/scratch/stefan/7769818/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC(Cl)=C(OC(C)C(=O)[O-])C(OC)=C2)=C1) `REAL300000237121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237121 none COC1=NOC(C(=O)C=CC2=CC(Cl)=C(OC(C)C(=O)[O-])C(OC)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', '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, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 70, 70, 70, 70, 34, 7, 33, 7, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 19, 19, 1, 1, 3, 1, 70, 82, 82, 82, 7, 7, 1, 12, 13, 12, 13, 4, 4, 4, 1, 70] 201 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 15, 21, 22, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 23, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 226 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237121 none COC1=NOC(C(=O)C=CC2=CC(Cl)=C(OC(C)C(=O)[O-])C(OC)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', '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, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 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, 7, 7, 25, 26, 70, 70, 70, 69, 69, 144, 186, 186, 201, 201, 70, 70, 120, 70, 1, 3, 3, 3, 25, 25, 70, 186, 186, 186, 186, 120, 120, 120, 70, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 606 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237121 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237121 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237121/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237121 Building REAL300000237122 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237122' /scratch/stefan/7769818/working/building/REAL300000237122 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237122 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237122/0 /scratch/stefan/7769818/working/building/REAL300000237122 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/122 `/scratch/stefan/7769818/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC(C(=O)[O-])=C(Cl)S2)=C1) `REAL300000237122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237122 none COC1=NOC(C(=O)C=CC2=CC(C(=O)[O-])=C(Cl)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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: [201, 157, 157, 155, 157, 76, 13, 75, 13, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 157, 201, 201, 201, 13, 13, 1, 157] 201 rigid atoms, others: [9, 10, 11, 12, 13, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 19, 20, 21, 22, 23, 24, 26]) total number of confs: 399 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237122 none COC1=NOC(C(=O)C=CC2=CC(C(=O)[O-])=C(Cl)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 157, 157, 157, 167, 167, 156, 157, 157, 1, 3, 3, 3, 50, 50, 157, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237122 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237122 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237122/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237122 Building REAL300000237123 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237123' /scratch/stefan/7769818/working/building/REAL300000237123 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237123 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237123/0 /scratch/stefan/7769818/working/building/REAL300000237123 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/123 `/scratch/stefan/7769818/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)=C1) `REAL300000237123.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237123 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 145, 145, 145, 145, 76, 12, 76, 12, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 7, 7, 7, 7, 1, 145, 166, 166, 166, 12, 12, 1, 1, 7, 7, 7, 7, 145] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237123 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 157, 62, 157, 62, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 201, 201, 201, 201, 62, 62, 7, 7, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) 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: REAL300000237123 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 49, 49, 145, 145, 145, 145, 201, 201, 145, 145, 201, 201, 201, 201, 145, 1, 2, 2, 2, 49, 49, 145, 145, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 24, 36] set([0, 7, 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, 35]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237123 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237123 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237123/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237123 Building REAL300000237124 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237124' /scratch/stefan/7769818/working/building/REAL300000237124 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237124 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237124/0 /scratch/stefan/7769818/working/building/REAL300000237124 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/124 `/scratch/stefan/7769818/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1) `REAL300000237124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237124 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 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: [108, 90, 90, 90, 90, 47, 12, 47, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 13, 12, 1, 89, 108, 108, 108, 12, 12, 1, 1, 12, 12, 24, 12, 89] 402 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237124 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 151, 75, 151, 75, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 75, 74, 12, 12, 1, 1, 2, 1, 201] 402 rigid atoms, others: [33, 34, 36, 13, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 37]) total number of confs: 451 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: REAL300000237124 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 10, 10, 42, 43, 89, 90, 90, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 1, 3, 3, 3, 42, 42, 89, 88, 201, 201, 402, 201, 1] 402 rigid atoms, others: [1, 2, 3, 4, 5, 6, 25, 37] set([0, 7, 8, 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]) total number of confs: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237124 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237124 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237124/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237124 Building REAL300000237125 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237125' /scratch/stefan/7769818/working/building/REAL300000237125 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237125 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237125/0 /scratch/stefan/7769818/working/building/REAL300000237125 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/125 `/scratch/stefan/7769818/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=C1) `REAL300000237125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237125 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 107, 107, 107, 107, 60, 13, 59, 13, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 12, 1, 107, 118, 118, 118, 13, 13, 1, 1, 12, 12, 12, 12, 107] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237125 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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 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, 167, 92, 166, 92, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 92, 92, 12, 12, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 490 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: REAL300000237125 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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 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, 9, 9, 27, 27, 107, 107, 107, 107, 201, 201, 201, 201, 201, 201, 201, 201, 107, 1, 3, 3, 3, 27, 27, 107, 107, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 24, 36] set([0, 7, 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, 35]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237125 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237125 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237125/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237125 Building REAL300000237126 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237126' /scratch/stefan/7769818/working/building/REAL300000237126 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237126 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237126/0 /scratch/stefan/7769818/working/building/REAL300000237126 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/126 `/scratch/stefan/7769818/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC(C(=O)[O-])=CC=C2OC)=C1) `REAL300000237126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237126 none COC1=NOC(C(=O)C=CC2=CC(C(=O)[O-])=CC=C2OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 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] 0 hydrogens 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, 164, 164, 164, 71, 9, 71, 9, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 3, 164, 201, 201, 201, 9, 9, 1, 1, 1, 3, 3, 3, 164] 201 rigid atoms, others: [9, 10, 11, 12, 13, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 379 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237126 none COC1=NOC(C(=O)C=CC2=CC(C(=O)[O-])=CC=C2OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 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] 0 hydrogens 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, 10, 10, 55, 56, 164, 164, 164, 164, 164, 164, 164, 164, 164, 187, 1, 3, 3, 3, 55, 55, 164, 164, 164, 187, 187, 187, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 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]) total number of confs: 328 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237126 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237126 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237126/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237126 Building REAL300000237127 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237127' /scratch/stefan/7769818/working/building/REAL300000237127 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237127 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237127/0 /scratch/stefan/7769818/working/building/REAL300000237127 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/127 `/scratch/stefan/7769818/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CSC3=CC=C(C(=O)[O-])C=C23)=C1) `REAL300000237127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237127 none COC1=NOC(C(=O)C=CC2=CSC3=CC=C(C(=O)[O-])C=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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] 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, 136, 136, 136, 136, 60, 9, 60, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 136, 141, 141, 141, 9, 9, 1, 1, 1, 1, 136] 141 rigid atoms, others: [9, 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, 32, 22, 23, 24, 25, 26, 27]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237127 none COC1=NOC(C(=O)C=CC2=CSC3=CC=C(C(=O)[O-])C=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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] 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: [2, 1, 1, 1, 1, 1, 1, 13, 13, 66, 66, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 1, 2, 2, 2, 66, 66, 136, 136, 136, 136, 1] 141 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 22] set([0, 7, 8, 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: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237127 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237127 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237127/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237127 Building REAL300000237128 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237128' /scratch/stefan/7769818/working/building/REAL300000237128 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237128 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237128/0 /scratch/stefan/7769818/working/building/REAL300000237128 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/128 `/scratch/stefan/7769818/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC(C(=O)[O-])=CC=C2Br)=C1) `REAL300000237128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237128 none COC1=NOC(C(=O)C=CC2=CC(C(=O)[O-])=CC=C2Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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] 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, 102, 102, 102, 102, 50, 9, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 102, 107, 107, 107, 9, 9, 1, 1, 1, 102] 107 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 204 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237128 none COC1=NOC(C(=O)C=CC2=CC(C(=O)[O-])=CC=C2Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 13, 13, 51, 51, 102, 102, 102, 102, 102, 102, 102, 102, 102, 1, 3, 3, 3, 51, 51, 100, 102, 102, 1] 107 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 213 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237128 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237128 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237128/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237128 Building REAL300000237129 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237129' /scratch/stefan/7769818/working/building/REAL300000237129 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237129 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237129/0 /scratch/stefan/7769818/working/building/REAL300000237129 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/129 `/scratch/stefan/7769818/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2[N+](=O)[O-])=C1) `REAL300000237129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237129 none COC1=NOC(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2[N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 85, 85, 85, 85, 39, 5, 39, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 85, 89, 89, 89, 5, 5, 1, 1, 1, 85] 89 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 171 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237129 none COC1=NOC(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2[N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 12, 12, 54, 55, 85, 85, 64, 80, 85, 85, 85, 85, 85, 85, 85, 1, 3, 3, 3, 54, 54, 85, 85, 85, 1] 89 rigid atoms, others: [1, 2, 3, 4, 5, 6, 22, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237129 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237129 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237129/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237129 Building REAL300000237130 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237130' /scratch/stefan/7769818/working/building/REAL300000237130 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237130 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237130/0 /scratch/stefan/7769818/working/building/REAL300000237130 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/130 `/scratch/stefan/7769818/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(C(=O)[O-])C(OC)=C2)=C1) `REAL300000237130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237130 none COC1=NOC(C(=O)C=CC2=CC=C(C(=O)[O-])C(OC)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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] 0 hydrogens 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, 132, 132, 132, 132, 40, 5, 40, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 1, 132, 170, 170, 170, 5, 5, 1, 1, 3, 3, 3, 1, 132] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 17, 18, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33]) total number of confs: 296 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237130 none COC1=NOC(C(=O)C=CC2=CC=C(C(=O)[O-])C(OC)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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] 0 hydrogens 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, 11, 11, 61, 61, 132, 132, 132, 132, 175, 175, 132, 132, 165, 132, 1, 2, 2, 2, 61, 61, 132, 132, 165, 165, 165, 132, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 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]) total number of confs: 495 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237130 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237130 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237130/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237130 Building REAL300000237131 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237131' /scratch/stefan/7769818/working/building/REAL300000237131 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237131 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237131/0 /scratch/stefan/7769818/working/building/REAL300000237131 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/131 `/scratch/stefan/7769818/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=C(F)C=C(C(=O)[O-])C=C2F)=C1) `REAL300000237131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237131 none COC1=NOC(C(=O)C=CC2=C(F)C=C(C(=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 53, 53, 53, 53, 34, 10, 34, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 60, 60, 60, 10, 10, 1, 1, 53] 60 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 126 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237131 none COC1=NOC(C(=O)C=CC2=C(F)C=C(C(=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 13, 13, 36, 36, 52, 52, 52, 48, 52, 52, 52, 52, 52, 52, 1, 3, 3, 3, 36, 36, 52, 52, 1] 59 rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237131 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237131 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237131/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237131 Building REAL300000237132 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237132' /scratch/stefan/7769818/working/building/REAL300000237132 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237132 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237132/0 /scratch/stefan/7769818/working/building/REAL300000237132 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/132 `/scratch/stefan/7769818/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=C(F)C=CC(C(=O)[O-])=C2F)=C1) `REAL300000237132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237132 none COC1=NOC(C(=O)C=CC2=C(F)C=CC(C(=O)[O-])=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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] 0 hydrogens 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, 164, 164, 164, 74, 11, 74, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 164, 201, 201, 201, 11, 11, 1, 1, 164] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 384 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237132 none COC1=NOC(C(=O)C=CC2=C(F)C=CC(C(=O)[O-])=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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] 0 hydrogens 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, 13, 13, 63, 63, 164, 164, 164, 164, 164, 164, 196, 196, 164, 164, 1, 2, 2, 2, 63, 63, 164, 164, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 421 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237132 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237132 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237132/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237132 Building REAL300000237133 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237133' /scratch/stefan/7769818/working/building/REAL300000237133 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237133 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237133/0 /scratch/stefan/7769818/working/building/REAL300000237133 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/133 `/scratch/stefan/7769818/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC(I)=CC(C(=O)[O-])=C2)=C1) `REAL300000237133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237133 none COC1=NOC(C(=O)C=CC2=CC(I)=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 80, 80, 80, 80, 37, 5, 37, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80, 96, 96, 96, 5, 5, 1, 1, 1, 80] 96 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 182 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237133 none COC1=NOC(C(=O)C=CC2=CC(I)=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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] 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, 12, 12, 38, 39, 80, 80, 80, 80, 80, 80, 80, 80, 80, 1, 3, 3, 3, 38, 38, 80, 80, 80, 1] 96 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237133 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237133 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237133/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237133 Building REAL300000237134 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237134' /scratch/stefan/7769818/working/building/REAL300000237134 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237134 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237134/0 /scratch/stefan/7769818/working/building/REAL300000237134 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/134 `/scratch/stefan/7769818/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=C1) `REAL300000237134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237134 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 59, 59, 59, 59, 20, 4, 20, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 23, 23, 5, 1, 1, 59, 71, 71, 71, 4, 4, 1, 1, 5, 5, 5, 9, 9, 5, 1, 1, 59] 201 rigid atoms, others: [32, 33, 40, 9, 10, 11, 12, 13, 14, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 196 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237134 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 144, 144, 144, 144, 73, 13, 73, 13, 2, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 5, 5, 144, 157, 157, 157, 13, 13, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5, 144] 201 rigid atoms, others: [34, 35, 36, 39, 13, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 40, 41, 42]) total number of confs: 328 number of broken/clashed sets: 7 ./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: REAL300000237134 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 9, 9, 38, 38, 59, 59, 38, 38, 144, 144, 138, 144, 144, 199, 201, 201, 144, 59, 59, 1, 3, 3, 3, 38, 38, 59, 59, 144, 144, 144, 199, 199, 144, 59, 59, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 42, 26] set([0, 7, 8, 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, 39, 40, 41]) total number of confs: 701 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237134 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237134 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237134/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237134 Building REAL300000237135 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237135' /scratch/stefan/7769818/working/building/REAL300000237135 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237135 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237135/0 /scratch/stefan/7769818/working/building/REAL300000237135 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/135 `/scratch/stefan/7769818/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC(=O)C2=CC(OC)=NO2)=CC=C1OCC(=O)[O-]) `REAL300000237135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237135 none CCOC1=CC(C=CC(=O)C2=CC(OC)=NO2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.2', 'O.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, 5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 12, 5, 8, 12, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 18, 18, 18, 6, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 18, 18, 17, 18, 69, 158, 182, 182, 93, 93, 93, 93, 93, 18, 5, 5, 1, 1, 1, 1, 18, 18, 158, 158] 201 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]) total number of confs: 844 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237135 none CCOC1=CC(C=CC(=O)C2=CC(OC)=NO2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.2', 'O.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, 5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 12, 5, 8, 12, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 5, 5, 13, 13, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 9, 39, 64, 64, 28, 28, 28, 28, 28, 1, 5, 5, 18, 18, 18, 18, 1, 1, 39, 39] 201 rigid atoms, others: [2, 3, 4, 5, 6, 17, 18, 19, 20, 38, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 338 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237135 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237135 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237135/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237135 Building REAL300000237136 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237136' /scratch/stefan/7769818/working/building/REAL300000237136 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237136 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237136/0 /scratch/stefan/7769818/working/building/REAL300000237136 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/136 `/scratch/stefan/7769818/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC(F)=C(C(=O)[O-])C(F)=C2)=C1) `REAL300000237136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237136 none COC1=NOC(C(=O)C=CC2=CC(F)=C(C(=O)[O-])C(F)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 44, 44, 44, 44, 19, 4, 19, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 44, 56, 56, 56, 4, 4, 1, 1, 44] 56 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 109 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237136 none COC1=NOC(C(=O)C=CC2=CC(F)=C(C(=O)[O-])C(F)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 11, 11, 33, 33, 43, 43, 43, 33, 33, 51, 51, 43, 43, 43, 1, 3, 3, 3, 33, 33, 43, 43, 1] 55 rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 203 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237136 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237136 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237136/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237136 Building REAL300000237137 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237137' /scratch/stefan/7769818/working/building/REAL300000237137 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237137 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237137/0 /scratch/stefan/7769818/working/building/REAL300000237137 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/137 `/scratch/stefan/7769818/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC3=C(C=C(C(=O)[O-])N3)O2)=C1) `REAL300000237137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237137 none COC1=NOC(C(=O)C=CC2=CC3=C(C=C(C(=O)[O-])N3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 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, 36, 36, 36, 36, 25, 9, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 36, 39, 39, 39, 9, 9, 1, 1, 1, 36] 39 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237137 none COC1=NOC(C(=O)C=CC2=CC3=C(C=C(C(=O)[O-])N3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 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: [3, 1, 1, 1, 1, 1, 1, 6, 6, 18, 19, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 3, 3, 3, 19, 18, 36, 36, 36, 1] 39 rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237137 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237137 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237137/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237137 Building REAL300000237138 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237138' /scratch/stefan/7769818/working/building/REAL300000237138 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237138 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237138/0 /scratch/stefan/7769818/working/building/REAL300000237138 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/138 `/scratch/stefan/7769818/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)=C1) `REAL300000237138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237138 none COC1=NOC(C(=O)C=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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] 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, 63, 63, 63, 63, 32, 6, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 63, 67, 67, 67, 6, 6, 1, 1, 1, 1, 63] 67 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 32, 22, 23, 24, 25, 26, 27]) total number of confs: 137 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237138 none COC1=NOC(C(=O)C=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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] 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, 1, 1, 1, 1, 1, 11, 11, 33, 33, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1, 3, 3, 3, 33, 33, 63, 63, 63, 63, 1] 67 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 22] set([0, 7, 8, 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: 137 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237138 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237138 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237138/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237138 Building REAL300000237139 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237139' /scratch/stefan/7769818/working/building/REAL300000237139 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237139 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237139/0 /scratch/stefan/7769818/working/building/REAL300000237139 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/139 `/scratch/stefan/7769818/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=CN3C(C(=O)[O-])=CN=C23)=C1) `REAL300000237139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237139 none COC1=NOC(C(=O)C=CC2=CC=CN3C(C(=O)[O-])=CN=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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] 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, 108, 108, 108, 108, 60, 11, 60, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 111, 111, 111, 11, 11, 1, 1, 1, 1, 108] 111 rigid atoms, others: [9, 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, 32, 22, 23, 24, 25, 26, 27]) total number of confs: 222 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237139 none COC1=NOC(C(=O)C=CC2=CC=CN3C(C(=O)[O-])=CN=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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] 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: [2, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 1, 3, 3, 3, 50, 50, 108, 108, 108, 108, 1] 111 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 22] set([0, 7, 8, 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: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237139 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237139 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237139/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237139 Building REAL300000237140 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237140' /scratch/stefan/7769818/working/building/REAL300000237140 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237140 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237140/0 /scratch/stefan/7769818/working/building/REAL300000237140 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/140 `/scratch/stefan/7769818/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=NC3=CC=CC=C3C(C(=O)[O-])=C2C)=C1) `REAL300000237140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237140 none COC1=NOC(C(=O)C=CC2=NC3=CC=CC=C3C(C(=O)[O-])=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.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', '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, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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] 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, 44, 10, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 72, 72, 72, 72, 10, 10, 1, 1, 1, 1, 2, 2, 2, 72] 72 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 37, 35, 20, 21, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237140 none COC1=NOC(C(=O)C=CC2=NC3=CC=CC=C3C(C(=O)[O-])=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.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', '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, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 12, 12, 32, 33, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 1, 3, 3, 3, 32, 32, 72, 72, 72, 72, 72, 72, 72, 1] 72 rigid atoms, others: [1, 2, 3, 4, 5, 6, 24, 37] set([0, 7, 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, 35, 36]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237140 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237140 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237140/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237140 Building REAL300000237141 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237141' /scratch/stefan/7769818/working/building/REAL300000237141 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237141 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237141/0 /scratch/stefan/7769818/working/building/REAL300000237141 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/141 `/scratch/stefan/7769818/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CN=C3C=CC(C(=O)[O-])=CN23)=C1) `REAL300000237141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237141 none COC1=NOC(C(=O)C=CC2=CN=C3C=CC(C(=O)[O-])=CN23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [152, 147, 147, 147, 147, 69, 11, 69, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 147, 152, 152, 152, 11, 11, 1, 1, 1, 1, 147] 152 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 32, 22, 23, 24, 25, 26, 27]) total number of confs: 288 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237141 none COC1=NOC(C(=O)C=CC2=CN=C3C=CC(C(=O)[O-])=CN23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 13, 13, 57, 57, 147, 147, 147, 147, 147, 147, 147, 147, 147, 147, 147, 1, 2, 2, 2, 57, 57, 147, 147, 147, 147, 1] 152 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 22] set([0, 7, 8, 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: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237141 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237141 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237141/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237141 Building REAL300000237142 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237142' /scratch/stefan/7769818/working/building/REAL300000237142 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237142 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237142/0 /scratch/stefan/7769818/working/building/REAL300000237142 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/142 `/scratch/stefan/7769818/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(N3C=NC(C(=O)[O-])=C3)C=C2)=C1) `REAL300000237142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237142 none COC1=NOC(C(=O)C=CC2=CC=C(N3C=NC(C(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [64, 51, 51, 51, 51, 19, 3, 19, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 51, 64, 64, 64, 3, 3, 1, 1, 8, 8, 1, 1, 51] 88 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 36]) total number of confs: 123 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237142 none COC1=NOC(C(=O)C=CC2=CC=C(N3C=NC(C(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 88, 59, 14, 59, 14, 2, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 88, 88, 88, 88, 14, 14, 8, 8, 1, 1, 8, 8, 88] 88 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 215 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: REAL300000237142 none COC1=NOC(C(=O)C=CC2=CC=C(N3C=NC(C(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 1, 1, 1, 1, 1, 11, 11, 41, 41, 51, 51, 41, 41, 88, 88, 88, 88, 88, 88, 88, 51, 51, 1, 3, 3, 3, 41, 40, 51, 51, 88, 88, 51, 51, 1] 88 rigid atoms, others: [1, 2, 3, 4, 5, 6, 24, 36] set([0, 7, 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, 35]) total number of confs: 225 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237142 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237142 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237142/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237142 Building REAL300000237143 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237143' /scratch/stefan/7769818/working/building/REAL300000237143 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237143 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237143/0 /scratch/stefan/7769818/working/building/REAL300000237143 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/143 `/scratch/stefan/7769818/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=C1) `REAL300000237143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237143 none COC1=NOC(C(=O)C=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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: [63, 57, 57, 57, 57, 33, 5, 33, 5, 1, 1, 1, 1, 1, 1, 9, 35, 53, 53, 1, 1, 1, 57, 63, 63, 63, 5, 5, 1, 1, 35, 35, 1, 57] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 30, 31, 33]) total number of confs: 294 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237143 none COC1=NOC(C(=O)C=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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: [2, 1, 1, 1, 1, 1, 1, 6, 6, 20, 21, 57, 57, 39, 57, 141, 199, 201, 201, 57, 57, 57, 1, 2, 2, 2, 20, 20, 57, 57, 199, 199, 57, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 22] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 575 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237143 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237143 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237143/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237143 Building REAL300000237144 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237144' /scratch/stefan/7769818/working/building/REAL300000237144 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237144 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237144/0 /scratch/stefan/7769818/working/building/REAL300000237144 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/144 `/scratch/stefan/7769818/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)=C1) `REAL300000237144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237144 none COC1=NOC(C(=O)C=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', '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.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, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 11, 11, 11, 7, 3, 7, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1, 1, 11, 13, 13, 13, 3, 3, 1, 1, 9, 17, 17, 1, 1, 11] 45 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37]) total number of confs: 101 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237144 none COC1=NOC(C(=O)C=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', '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.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, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 11, 11, 8, 8, 19, 19, 19, 37, 45, 45, 45, 11, 11, 1, 3, 3, 3, 8, 7, 11, 11, 37, 45, 45, 11, 11, 1] 45 rigid atoms, others: [1, 2, 3, 4, 5, 6, 24, 37] set([0, 7, 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, 35, 36]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237144 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237144 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237144/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237144 Building REAL300000237145 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237145' /scratch/stefan/7769818/working/building/REAL300000237145 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237145 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237145/0 /scratch/stefan/7769818/working/building/REAL300000237145 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/145 `/scratch/stefan/7769818/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=CC=C3C(=O)[O-])C=C2)=C1) `REAL300000237145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237145 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=CC=C3C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [67, 53, 53, 53, 53, 20, 4, 20, 4, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 9, 9, 1, 1, 53, 67, 67, 67, 4, 4, 1, 1, 7, 7, 6, 7, 1, 1, 53] 115 rigid atoms, others: [32, 37, 38, 9, 10, 11, 12, 13, 14, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 39]) total number of confs: 135 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237145 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=CC=C3C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [115, 113, 113, 113, 113, 71, 14, 71, 14, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 113, 115, 115, 115, 14, 14, 7, 7, 1, 1, 1, 1, 7, 7, 113] 115 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 258 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: REAL300000237145 none COC1=NOC(C(=O)C=CC2=CC=C(C3=CC=CC=C3C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 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 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 11, 11, 38, 38, 53, 53, 38, 42, 113, 113, 109, 113, 113, 113, 115, 115, 53, 53, 1, 3, 3, 3, 38, 38, 53, 53, 113, 113, 110, 113, 53, 53, 1] 115 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 308 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237145 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237145 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237145/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237145 Building REAL300000237146 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237146' /scratch/stefan/7769818/working/building/REAL300000237146 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237146 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237146/0 /scratch/stefan/7769818/working/building/REAL300000237146 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/146 `/scratch/stefan/7769818/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2OC)=C1) `REAL300000237146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237146 none COC1=NOC(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 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, 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, 151, 151, 151, 151, 65, 10, 65, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 151, 171, 171, 171, 10, 10, 1, 1, 1, 4, 4, 4, 151] 171 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 324 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237146 none COC1=NOC(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 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, 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, 12, 12, 68, 68, 151, 151, 151, 151, 151, 151, 151, 151, 151, 154, 1, 3, 3, 3, 68, 68, 151, 151, 151, 154, 154, 154, 1] 171 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 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]) total number of confs: 290 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237146 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237146 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237146/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237146 Building REAL300000237147 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237147' /scratch/stefan/7769818/working/building/REAL300000237147 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237147 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237147/0 /scratch/stefan/7769818/working/building/REAL300000237147 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/147 `/scratch/stefan/7769818/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)C=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)=C1) `REAL300000237147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237147 none COC1=NOC(C(=O)C=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 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 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 150, 150, 62, 9, 62, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 150, 150, 150, 150, 9, 9, 1, 1, 1, 150] 150 rigid atoms, others: [9, 10, 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, 32, 23, 24, 25, 26, 27, 28]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237147 none COC1=NOC(C(=O)C=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 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 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 13, 13, 62, 62, 150, 150, 150, 150, 150, 150, 150, 150, 150, 150, 150, 150, 1, 2, 2, 2, 62, 62, 150, 150, 150, 1] 150 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 23] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237147 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237147 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237147/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237147 Building REAL300000237148 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237148' /scratch/stefan/7769818/working/building/REAL300000237148 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237148 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237148/0 /scratch/stefan/7769818/working/building/REAL300000237148 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/148 `/scratch/stefan/7769818/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1OCC(=O)[O-]) `REAL300000237148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237148 none COC1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 50, 50, 50, 17, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 138, 201, 201, 201, 85, 85, 85, 50, 17, 17, 1, 1, 1, 1, 1, 1, 50, 50, 201, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43]) total number of confs: 615 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237148 none COC1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 61, 61, 23, 23, 14, 2, 14, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 61, 61, 61, 61, 150, 201, 201, 201, 101, 101, 101, 61, 23, 23, 2, 2, 2, 1, 1, 2, 61, 61, 201, 201] 201 rigid atoms, others: [37, 38, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 593 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: REAL300000237148 none COC1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 9, 29, 35, 35, 3, 3, 3, 1, 5, 5, 50, 50, 50, 50, 50, 50, 1, 1, 29, 29] 201 rigid atoms, others: [1, 2, 3, 4, 5, 40, 41, 20, 21, 22, 23, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237148 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237148 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237148/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237148 Building REAL300000237149 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237149' /scratch/stefan/7769818/working/building/REAL300000237149 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237149 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237149/0 /scratch/stefan/7769818/working/building/REAL300000237149 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/149 `/scratch/stefan/7769818/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1) `REAL300000237149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237149 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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, 7, 7, 7, 7, 7, 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, 54, 55, 55, 54, 54, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 55, 55, 55, 55, 54, 54, 1, 1, 1, 5, 5, 1, 55, 55] 55 rigid atoms, others: [33, 9, 11, 12, 13, 14, 15, 16, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 32, 34, 35]) total number of confs: 145 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237149 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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, 7, 7, 7, 7, 7, 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, 21, 6, 21, 6, 5, 6, 6, 1, 1, 1, 1, 1, 1, 6, 55, 55, 55, 55, 55, 55, 5, 6, 6, 1, 1, 6, 55, 55] 55 rigid atoms, others: [32, 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, 33, 34, 35]) total number of confs: 138 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: REAL300000237149 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 18, 18, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 3, 3, 56, 56, 56, 56, 56, 56, 1, 1] 56 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 98 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237149 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237149 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237149/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237149 Building REAL300000237150 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237150' /scratch/stefan/7769818/working/building/REAL300000237150 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237150 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237150/0 /scratch/stefan/7769818/working/building/REAL300000237150 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/150 `/scratch/stefan/7769818/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1) `REAL300000237150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237150 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 59, 37, 85, 85, 37, 37, 12, 1, 12, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 85, 85, 201, 201, 85, 85, 37, 37, 1, 1, 1, 4, 4, 1, 85, 85] 201 rigid atoms, others: [32, 33, 34, 37, 11, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 38, 39]) total number of confs: 793 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237150 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 149, 74, 49, 100, 100, 49, 49, 27, 5, 27, 5, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 100, 100, 201, 201, 100, 100, 49, 49, 4, 5, 5, 1, 1, 5, 100, 100] 201 rigid atoms, others: [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, 34, 37, 38, 39]) total number of confs: 779 number of broken/clashed sets: 6 ./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: REAL300000237150 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 19, 3, 1, 1, 1, 1, 1, 1, 5, 5, 29, 29, 85, 85, 85, 85, 85, 86, 86, 86, 86, 85, 1, 1, 11, 11, 1, 1, 5, 5, 85, 85, 85, 86, 86, 85, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 24, 25, 38, 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]) total number of confs: 200 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237150 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237150 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237150/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237150 Building REAL300000237151 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237151' /scratch/stefan/7769818/working/building/REAL300000237151 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237151 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237151/0 /scratch/stefan/7769818/working/building/REAL300000237151 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/151 `/scratch/stefan/7769818/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1) `REAL300000237151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237151 none O=C([O-])CCOC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 192, 195, 140, 51, 30, 78, 78, 30, 30, 12, 1, 12, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 78, 78, 201, 201, 195, 195, 78, 78, 30, 30, 1, 1, 1, 4, 4, 1, 78, 78] 201 rigid atoms, others: [35, 36, 37, 40, 12, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 41, 42]) total number of confs: 750 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237151 none O=C([O-])CCOC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 193, 186, 118, 44, 29, 76, 76, 29, 29, 19, 4, 19, 4, 3, 4, 4, 1, 1, 1, 1, 1, 1, 4, 76, 76, 201, 201, 186, 186, 76, 76, 29, 29, 3, 4, 4, 1, 1, 4, 76, 76] 201 rigid atoms, others: [38, 39, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 827 number of broken/clashed sets: 39 ./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: REAL300000237151 none O=C([O-])CCOC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 16, 11, 3, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 78, 78, 78, 78, 78, 83, 83, 83, 83, 78, 1, 1, 13, 13, 11, 11, 1, 1, 5, 5, 78, 78, 78, 83, 83, 78, 1, 1] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 41, 25, 26, 42, 31] set([0, 1, 2, 3, 4, 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: 200 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237151 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237151 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237151/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237151 Building REAL300000237152 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237152' /scratch/stefan/7769818/working/building/REAL300000237152 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237152 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237152/0 /scratch/stefan/7769818/working/building/REAL300000237152 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/152 `/scratch/stefan/7769818/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1)C(=O)[O-]) `REAL300000237152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237152 none CC(OC1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 167, 59, 59, 59, 59, 59, 32, 32, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 59, 201, 201, 201, 201, 201, 201, 201, 59, 59, 59, 32, 32, 1, 1, 1, 4, 4, 1, 59] 201 rigid atoms, others: [36, 37, 38, 41, 10, 12, 13, 14, 15, 16, 17, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 42]) total number of confs: 484 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237152 none CC(OC1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [175, 140, 59, 59, 59, 59, 59, 33, 33, 20, 4, 20, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 59, 175, 175, 175, 175, 175, 175, 175, 59, 59, 59, 33, 33, 3, 4, 4, 1, 1, 4, 59] 175 rigid atoms, others: [39, 40, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 465 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: REAL300000237152 none CC(OC1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 12, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 59, 59, 59, 59, 59, 63, 63, 63, 63, 59, 1, 27, 38, 38, 27, 27, 27, 27, 1, 1, 1, 5, 5, 59, 59, 59, 63, 63, 59, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 42, 23, 31] set([0, 1, 9, 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, 41]) total number of confs: 221 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237152 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237152 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237152/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237152 Building REAL300000237153 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237153' /scratch/stefan/7769818/working/building/REAL300000237153 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237153 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237153/0 /scratch/stefan/7769818/working/building/REAL300000237153 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/153 `/scratch/stefan/7769818/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1) `REAL300000237153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237153 none O=C([O-])CCOC1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 191, 155, 40, 40, 40, 40, 40, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 40, 201, 201, 191, 191, 40, 40, 40, 17, 17, 1, 1, 1, 4, 4, 1, 40] 201 rigid atoms, others: [36, 37, 38, 41, 13, 15, 16, 17, 18, 19, 20, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 42]) total number of confs: 497 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237153 none O=C([O-])CCOC1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 189, 158, 51, 51, 51, 51, 51, 27, 27, 17, 5, 17, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 51, 201, 201, 189, 189, 51, 51, 51, 27, 27, 4, 5, 5, 1, 1, 5, 51] 201 rigid atoms, others: [39, 40, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 504 number of broken/clashed sets: 33 ./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: REAL300000237153 none O=C([O-])CCOC1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 22, 33, 18, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 40, 40, 40, 40, 40, 44, 44, 44, 44, 40, 1, 22, 22, 18, 18, 1, 1, 1, 5, 5, 40, 40, 40, 44, 44, 40, 1] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 26, 42, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 210 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237153 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237153 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237153/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237153 Building REAL300000237154 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237154' /scratch/stefan/7769818/working/building/REAL300000237154 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237154 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237154/0 /scratch/stefan/7769818/working/building/REAL300000237154 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/154 `/scratch/stefan/7769818/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)O2)C=C1) `REAL300000237154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237154 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 12, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 125, 201, 125, 201, 201, 125, 125, 125, 125, 83, 83, 31, 6, 31, 6, 5, 6, 6, 1, 1, 1, 1, 1, 1, 6, 125, 201, 201, 201, 201, 125, 125, 83, 83, 5, 6, 6, 1, 1, 6, 201, 201] 201 rigid atoms, others: [38, 39, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 885 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237154 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 12, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 44, 45, 117, 117, 117, 117, 117, 125, 125, 125, 125, 117, 1, 6, 6, 7, 7, 1, 1, 12, 12, 117, 117, 117, 125, 125, 117, 7, 7] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 26, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237154 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 12, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 117, 201, 117, 201, 201, 117, 117, 117, 117, 57, 57, 12, 1, 12, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 117, 201, 201, 201, 201, 117, 117, 57, 57, 1, 1, 1, 4, 4, 1, 201, 201] 201 rigid atoms, others: [35, 36, 37, 40, 13, 15, 16, 17, 18, 19, 20, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 41, 42]) total number of confs: 891 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: REAL300000237154 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 12, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 8, 8, 37, 37, 93, 93, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 9, 8, 37, 37, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237154 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237154 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237154/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237154 Building REAL300000237155 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237155' /scratch/stefan/7769818/working/building/REAL300000237155 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237155 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237155/0 /scratch/stefan/7769818/working/building/REAL300000237155 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/155 `/scratch/stefan/7769818/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1) `REAL300000237155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237155 none O=C([O-])COC1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 136, 55, 55, 55, 55, 55, 30, 30, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 55, 201, 201, 55, 55, 55, 30, 30, 1, 1, 1, 3, 3, 1, 55] 201 rigid atoms, others: [33, 34, 35, 38, 12, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 39]) total number of confs: 619 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237155 none O=C([O-])COC1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 152, 63, 63, 63, 63, 63, 38, 37, 24, 6, 25, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 63, 201, 201, 63, 63, 63, 38, 37, 6, 6, 6, 1, 1, 6, 63] 201 rigid atoms, others: [36, 37, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 563 number of broken/clashed sets: 17 ./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: REAL300000237155 none O=C([O-])COC1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 18, 27, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 55, 55, 55, 55, 55, 71, 71, 71, 71, 55, 1, 18, 18, 1, 1, 1, 5, 5, 55, 55, 55, 71, 71, 55, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 39, 25, 28, 29, 30] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 202 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237155 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237155 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237155/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237155 Building REAL300000237156 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237156' /scratch/stefan/7769818/working/building/REAL300000237156 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237156 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237156/0 /scratch/stefan/7769818/working/building/REAL300000237156 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/156 `/scratch/stefan/7769818/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1) `REAL300000237156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237156 none O=C([O-])C(F)(F)OC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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, 15, 15, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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, 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, 7, 7, 7] 0 hydrogens 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, 130, 201, 201, 34, 19, 58, 58, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 58, 58, 58, 58, 19, 19, 1, 1, 1, 4, 4, 1, 58, 58] 201 rigid atoms, others: [32, 33, 34, 37, 13, 15, 16, 17, 18, 19, 20, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 38, 39]) total number of confs: 709 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237156 none O=C([O-])C(F)(F)OC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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, 15, 15, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 146, 201, 201, 52, 30, 81, 81, 30, 30, 20, 5, 20, 5, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 81, 81, 81, 81, 30, 30, 4, 5, 5, 1, 1, 5, 81, 81] 201 rigid atoms, others: [35, 36, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 731 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: REAL300000237156 none O=C([O-])C(F)(F)OC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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, 15, 15, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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, 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, 7, 7, 7] 0 hydrogens 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, 23, 29, 6, 23, 23, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 58, 58, 58, 58, 58, 60, 60, 60, 60, 58, 1, 1, 1, 1, 5, 5, 58, 58, 58, 60, 60, 58, 1, 1] 201 rigid atoms, others: [38, 6, 7, 8, 9, 10, 11, 39, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237156 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237156 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237156/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237156 Building REAL300000237157 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237157' /scratch/stefan/7769818/working/building/REAL300000237157 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237157 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237157/0 /scratch/stefan/7769818/working/building/REAL300000237157 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/157 `/scratch/stefan/7769818/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1) `REAL300000237157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237157 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 199, 199, 199, 199, 199, 199, 199, 199, 199, 84, 84, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 199, 199, 201, 201, 201, 199, 84, 84, 1, 1, 1, 3, 3, 1, 199, 199] 201 rigid atoms, others: [35, 36, 37, 40, 14, 16, 17, 18, 19, 20, 21, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 41, 42]) total number of confs: 361 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237157 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 200, 201, 201, 201, 201, 201, 131, 131, 47, 7, 47, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 201, 201, 201, 201, 201, 201, 131, 130, 6, 7, 6, 1, 1, 7, 201, 201] 201 rigid atoms, others: [38, 39, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 443 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: REAL300000237157 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 11, 11, 56, 56, 199, 199, 199, 199, 199, 201, 201, 201, 201, 199, 1, 1, 3, 3, 3, 1, 11, 11, 199, 199, 199, 201, 201, 199, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 41, 27, 28, 42] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 322 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237157 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237157 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237157/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237157 Building REAL300000237158 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237158' /scratch/stefan/7769818/working/building/REAL300000237158 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237158 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237158/0 /scratch/stefan/7769818/working/building/REAL300000237158 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/158 `/scratch/stefan/7769818/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)N=N1) `REAL300000237158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237158 none O=C([O-])CN1C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 8, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 129, 129, 129, 57, 57, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 129, 129, 201, 201, 129, 57, 57, 1, 1, 1, 3, 3, 1] 201 rigid atoms, others: [34, 9, 11, 12, 13, 14, 15, 16, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 617 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237158 none O=C([O-])CN1C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 8, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 163, 163, 163, 101, 101, 37, 6, 38, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 163, 163, 201, 201, 163, 101, 101, 6, 6, 6, 1, 1, 6] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 573 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: REAL300000237158 none O=C([O-])CN1C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 8, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 1, 1, 1, 1, 1, 11, 11, 45, 45, 129, 129, 129, 129, 129, 144, 144, 144, 144, 129, 1, 1, 6, 6, 1, 11, 11, 129, 129, 129, 144, 144, 129] 201 rigid atoms, others: [3, 4, 5, 6, 7, 22, 23, 26] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237158 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237158 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237158/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237158 Building REAL300000237159 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237159' /scratch/stefan/7769818/working/building/REAL300000237159 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237159 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237159/0 /scratch/stefan/7769818/working/building/REAL300000237159 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/159 `/scratch/stefan/7769818/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1) `REAL300000237159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237159 none O=C([O-])C1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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, 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 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [154, 154, 154, 154, 153, 154, 154, 75, 75, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 154, 153, 154, 154, 75, 75, 1, 1, 1, 6, 6, 1, 154] 154 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 35]) total number of confs: 306 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237159 none O=C([O-])C1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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, 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 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [154, 154, 154, 154, 154, 154, 154, 123, 123, 46, 9, 46, 9, 8, 9, 9, 1, 1, 1, 1, 1, 1, 9, 154, 154, 154, 154, 123, 123, 8, 9, 9, 1, 1, 9, 154] 154 rigid atoms, others: [32, 33, 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, 34, 35]) total number of confs: 373 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: REAL300000237159 none O=C([O-])C1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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, 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 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 46, 47, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 1, 1, 1, 1, 7, 7, 154, 154, 154, 154, 154, 154, 1] 154 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 242 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237159 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237159 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237159/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237159 Building REAL300000237160 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237160' /scratch/stefan/7769818/working/building/REAL300000237160 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237160 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237160/0 /scratch/stefan/7769818/working/building/REAL300000237160 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/160 `/scratch/stefan/7769818/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1) `REAL300000237160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237160 none O=C([O-])C1=CSC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 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: [185, 185, 185, 185, 185, 185, 72, 72, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 185, 185, 72, 72, 1, 1, 1, 5, 5, 1, 185] 185 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 21, 26, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 32, 22, 23, 24, 25, 29, 30]) total number of confs: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237160 none O=C([O-])C1=CSC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 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, 174, 174, 174, 102, 102, 39, 6, 40, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 174, 174, 102, 102, 6, 6, 6, 1, 1, 6, 174] 174 rigid atoms, others: [15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 385 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: REAL300000237160 none O=C([O-])C1=CSC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 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, 1, 13, 13, 93, 93, 185, 185, 185, 185, 185, 185, 185, 185, 185, 185, 1, 1, 13, 13, 185, 185, 185, 185, 185, 185, 1] 185 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 22, 23] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237160 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237160 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237160/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237160 Building REAL300000237161 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237161' /scratch/stefan/7769818/working/building/REAL300000237161 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237161 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237161/0 /scratch/stefan/7769818/working/building/REAL300000237161 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/161 `/scratch/stefan/7769818/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1OCCC(=O)[O-]) `REAL300000237161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237161 none COC1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 56, 56, 56, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 56, 56, 56, 56, 145, 193, 193, 201, 185, 96, 96, 96, 56, 17, 17, 1, 1, 1, 3, 3, 1, 56, 56, 193, 193, 193, 193] 201 rigid atoms, others: [35, 36, 37, 7, 40, 9, 10, 11, 12, 13, 14, 19] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 613 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237161 none COC1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 60, 60, 60, 21, 21, 11, 2, 11, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 60, 60, 60, 60, 144, 191, 191, 201, 184, 98, 98, 98, 60, 21, 21, 2, 2, 2, 1, 1, 2, 60, 60, 191, 191, 191, 191] 201 rigid atoms, others: [38, 39, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 616 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: REAL300000237161 none COC1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 56, 56, 56, 56, 56, 58, 58, 58, 58, 56, 1, 1, 1, 1, 9, 14, 15, 26, 24, 3, 3, 3, 1, 5, 5, 56, 56, 56, 58, 58, 56, 1, 1, 14, 14, 14, 14] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 41, 42, 20, 21, 22, 23] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237161 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237161 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237161/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237161 Building REAL300000237162 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237162' /scratch/stefan/7769818/working/building/REAL300000237162 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237162 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237162/0 /scratch/stefan/7769818/working/building/REAL300000237162 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/162 `/scratch/stefan/7769818/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C(Cl)=C1) `REAL300000237162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237162 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 127, 147, 147, 86, 86, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 147, 147, 147, 147, 147, 86, 86, 1, 1, 1, 5, 5, 1, 147] 147 rigid atoms, others: [34, 9, 11, 12, 13, 14, 15, 16, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 35]) total number of confs: 396 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237162 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 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, 145, 149, 149, 111, 111, 42, 8, 42, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 149, 149, 149, 149, 149, 111, 111, 8, 8, 8, 1, 1, 8, 149] 149 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 369 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: REAL300000237162 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 61, 61, 147, 147, 147, 147, 147, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 9, 9, 147, 147, 147, 147, 147, 147, 1] 147 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 266 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237162 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237162 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237162/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237162 Building REAL300000237163 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237163' /scratch/stefan/7769818/working/building/REAL300000237163 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237163 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237163/0 /scratch/stefan/7769818/working/building/REAL300000237163 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/163 `/scratch/stefan/7769818/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1) `REAL300000237163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237163 none O=C([O-])C1=C(Cl)C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 85, 85, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 201, 201, 201, 85, 85, 1, 1, 1, 3, 3, 1, 201, 201, 201] 201 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16, 21, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 33, 34, 35]) total number of confs: 370 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237163 none O=C([O-])C1=C(Cl)C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 142, 142, 53, 6, 53, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 201, 201, 201, 142, 141, 6, 6, 6, 1, 1, 6, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 30, 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, 32, 33, 34, 35]) total number of confs: 458 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: REAL300000237163 none O=C([O-])C1=C(Cl)C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 9, 9, 72, 72, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 9, 9, 201, 201, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 22, 23, 24, 33] 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]) total number of confs: 341 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237163 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237163 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237163/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237163 Building REAL300000237164 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237164' /scratch/stefan/7769818/working/building/REAL300000237164 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237164 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237164/0 /scratch/stefan/7769818/working/building/REAL300000237164 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/164 `/scratch/stefan/7769818/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1O) `REAL300000237164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237164 none O=C([O-])C1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 394 conformations in input total number of sets (complete confs): 394 using faster count positions algorithm for large data unique positions, atoms: [197, 193, 197, 193, 193, 90, 90, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 193, 193, 193, 193, 193, 90, 90, 1, 1, 1, 5, 5, 1, 193, 193, 386] 394 rigid atoms, others: [33, 8, 10, 11, 12, 13, 14, 15, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 34, 35, 36]) total number of confs: 774 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237164 none O=C([O-])C1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 378 conformations in input total number of sets (complete confs): 378 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 189, 189, 189, 145, 145, 40, 6, 41, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 189, 189, 189, 189, 189, 145, 145, 6, 6, 6, 1, 1, 6, 189, 189, 378] 378 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 820 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: REAL300000237164 none O=C([O-])C1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 394 conformations in input total number of sets (complete confs): 394 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 5, 5, 44, 44, 193, 193, 193, 193, 193, 197, 197, 197, 197, 193, 1, 1, 1, 1, 1, 5, 5, 193, 193, 193, 197, 197, 193, 1, 1, 2] 394 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 301 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237164 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237164 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237164/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237164 Building REAL300000237165 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237165' /scratch/stefan/7769818/working/building/REAL300000237165 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237165 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237165/0 /scratch/stefan/7769818/working/building/REAL300000237165 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/165 `/scratch/stefan/7769818/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1) `REAL300000237165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237165 none CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 199, 199, 199, 199, 199, 199, 199, 199, 86, 86, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 199, 199, 199, 199, 199, 199, 199, 199, 86, 86, 1, 1, 1, 5, 5, 1] 199 rigid atoms, others: [36, 37, 38, 41, 13, 15, 16, 17, 18, 19, 20, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40]) total number of confs: 379 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237165 none CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 188, 188, 188, 188, 188, 188, 188, 188, 143, 143, 48, 8, 49, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 188, 188, 188, 188, 188, 188, 188, 188, 143, 143, 8, 8, 8, 1, 1, 8] 188 rigid atoms, others: [39, 40, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 419 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: REAL300000237165 none CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 61, 61, 199, 199, 199, 199, 199, 199, 199, 199, 199, 199, 2, 2, 2, 1, 2, 2, 2, 1, 9, 9, 199, 199, 199, 199, 199, 199] 199 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 29] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 338 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237165 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237165 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237165/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237165 Building REAL300000237166 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237166' /scratch/stefan/7769818/working/building/REAL300000237166 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237166 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237166/0 /scratch/stefan/7769818/working/building/REAL300000237166 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/166 `/scratch/stefan/7769818/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1)C(=O)[O-]) `REAL300000237166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237166 none CC(OC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 166, 56, 31, 91, 91, 31, 31, 12, 1, 12, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 91, 91, 201, 201, 201, 201, 201, 201, 201, 91, 91, 31, 31, 1, 1, 1, 4, 4, 1, 91, 91] 201 rigid atoms, others: [35, 36, 37, 40, 9, 11, 12, 13, 14, 15, 16, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 41, 42]) total number of confs: 695 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237166 none CC(OC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 159, 73, 51, 108, 108, 51, 51, 24, 5, 24, 5, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 108, 108, 201, 201, 201, 201, 201, 201, 201, 108, 108, 51, 51, 4, 5, 5, 1, 1, 5, 108, 108] 201 rigid atoms, others: [38, 39, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 759 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: REAL300000237166 none CC(OC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 5, 5, 23, 23, 91, 91, 91, 91, 91, 96, 96, 96, 96, 91, 1, 1, 13, 18, 18, 13, 13, 13, 13, 1, 1, 5, 5, 91, 91, 91, 96, 96, 91, 1, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 41, 42, 22, 23, 31] set([0, 1, 8, 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, 40]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237166 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237166 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237166/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237166 Building REAL300000237167 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237167' /scratch/stefan/7769818/working/building/REAL300000237167 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237167 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237167/0 /scratch/stefan/7769818/working/building/REAL300000237167 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/167 `/scratch/stefan/7769818/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1) `REAL300000237167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237167 none O=C([O-])CCOC1=CC=CC=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 198, 185, 120, 63, 63, 63, 39, 63, 63, 25, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 201, 201, 185, 185, 63, 63, 63, 63, 25, 25, 1, 1, 1, 2, 2, 1] 201 rigid atoms, others: [37, 38, 39, 42, 14, 16, 17, 18, 19, 20, 21, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41]) total number of confs: 730 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237167 none O=C([O-])CCOC1=CC=CC=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 197, 191, 155, 105, 105, 105, 78, 105, 105, 74, 74, 40, 6, 40, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 201, 201, 191, 191, 105, 105, 105, 105, 74, 74, 6, 6, 6, 1, 1, 6] 201 rigid atoms, others: [40, 41, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 718 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: REAL300000237167 none O=C([O-])CCOC1=CC=CC=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 66, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 63, 63, 63, 63, 63, 64, 64, 64, 64, 63, 49, 49, 30, 30, 1, 1, 1, 1, 7, 7, 63, 63, 63, 64, 64, 63] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 382 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237167 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237167 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237167/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237167 Building REAL300000237168 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237168' /scratch/stefan/7769818/working/building/REAL300000237168 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237168 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237168/0 /scratch/stefan/7769818/working/building/REAL300000237168 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/168 `/scratch/stefan/7769818/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)[O-])=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1) `REAL300000237168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237168 none CN1N=CC(C(=O)[O-])=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 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, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 78, 78, 79, 79, 57, 57, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 78, 78, 78, 78, 57, 57, 1, 1, 1, 3, 3, 1] 79 rigid atoms, others: [32, 35, 11, 13, 14, 15, 16, 17, 18, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 184 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237168 none CN1N=CC(C(=O)[O-])=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 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, 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 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, 79, 75, 75, 35, 6, 36, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 79, 79, 79, 79, 75, 75, 6, 6, 6, 1, 1, 6] 79 rigid atoms, others: [33, 34, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 204 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: REAL300000237168 none CN1N=CC(C(=O)[O-])=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 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, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 9, 9, 28, 28, 78, 78, 78, 78, 78, 79, 79, 79, 79, 78, 2, 2, 2, 1, 9, 9, 78, 78, 78, 79, 79, 78] 79 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 27] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237168 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237168 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237168/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237168 Building REAL300000237169 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237169' /scratch/stefan/7769818/working/building/REAL300000237169 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237169 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237169/0 /scratch/stefan/7769818/working/building/REAL300000237169 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/169 `/scratch/stefan/7769818/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1F) `REAL300000237169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237169 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 201, 197, 197, 197, 85, 85, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 197, 197, 197, 197, 197, 85, 85, 1, 1, 1, 3, 3, 1, 197] 201 rigid atoms, others: [34, 9, 11, 12, 13, 14, 15, 16, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 35]) total number of confs: 387 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237169 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 121, 121, 44, 6, 45, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 201, 201, 201, 201, 201, 121, 121, 6, 6, 6, 1, 1, 6, 201] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 457 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: REAL300000237169 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 49, 49, 197, 197, 197, 197, 197, 201, 201, 201, 201, 197, 1, 1, 1, 1, 1, 6, 6, 197, 197, 197, 201, 201, 197, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25, 26] 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]) total number of confs: 312 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237169 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237169 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237169/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237169 Building REAL300000237170 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237170' /scratch/stefan/7769818/working/building/REAL300000237170 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237170 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237170/0 /scratch/stefan/7769818/working/building/REAL300000237170 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/170 `/scratch/stefan/7769818/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)O1) `REAL300000237170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237170 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 12, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 130, 130, 130, 130, 60, 60, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 130, 201, 201, 130, 130, 60, 60, 1, 1, 1, 3, 3, 1] 201 rigid atoms, others: [32, 33, 36, 11, 13, 14, 15, 16, 17, 18, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 488 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237170 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 12, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [143, 143, 143, 143, 96, 96, 96, 96, 66, 66, 34, 6, 35, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 96, 143, 143, 96, 96, 66, 66, 6, 6, 6, 1, 1, 6] 143 rigid atoms, others: [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, 33, 36]) total number of confs: 392 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: REAL300000237170 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 12, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 13, 32, 13, 1, 1, 1, 1, 1, 1, 12, 12, 37, 37, 130, 130, 130, 130, 130, 139, 139, 139, 139, 130, 1, 13, 13, 1, 1, 12, 12, 130, 130, 130, 139, 139, 130] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 24, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237170 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237170 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237170/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237170 Building REAL300000237171 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237171' /scratch/stefan/7769818/working/building/REAL300000237171 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237171 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237171/0 /scratch/stefan/7769818/working/building/REAL300000237171 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/171 `/scratch/stefan/7769818/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1C(=O)[O-]) `REAL300000237171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237171 none COC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1C(=O)[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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 130, 130, 130, 130, 58, 58, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 201, 201, 201, 201, 201, 130, 130, 58, 58, 1, 1, 1, 1, 1, 1, 130] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39]) total number of confs: 675 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237171 none COC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1C(=O)[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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 134, 134, 134, 134, 88, 88, 22, 2, 23, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 134, 134, 134, 201, 201, 201, 201, 201, 134, 134, 88, 88, 2, 2, 2, 1, 1, 2, 134] 201 rigid atoms, others: [36, 37, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 706 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: REAL300000237171 none COC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1C(=O)[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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 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, 39, 39, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 1, 1, 1, 3, 3, 4, 4, 4, 1, 1, 5, 5, 130, 130, 130, 130, 130, 130, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 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]) total number of confs: 216 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237171 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237171 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237171/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237171 Building REAL300000237172 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237172' /scratch/stefan/7769818/working/building/REAL300000237172 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237172 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237172/0 /scratch/stefan/7769818/working/building/REAL300000237172 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/172 `/scratch/stefan/7769818/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1) `REAL300000237172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237172 none O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=CC=CC(N3C=NN=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.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, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 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, 201, 201, 201, 201, 201, 60, 60, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 201, 201, 201, 60, 60, 1, 1, 1, 3, 3, 1, 201] 201 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 32, 33, 35]) total number of confs: 337 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237172 none O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=CC=CC(N3C=NN=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.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, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 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, 201, 201, 201, 201, 201, 121, 121, 43, 6, 43, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 201, 201, 201, 121, 120, 6, 6, 6, 1, 1, 6, 201] 201 rigid atoms, others: [32, 33, 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, 34, 35]) 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: REAL300000237172 none O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=CC=CC(N3C=NN=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.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, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 82, 82, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 11, 11, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 24, 25, 26] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 348 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237172 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237172 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237172/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237172 Building REAL300000237173 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237173' /scratch/stefan/7769818/working/building/REAL300000237173 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237173 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237173/0 /scratch/stefan/7769818/working/building/REAL300000237173 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/173 `/scratch/stefan/7769818/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1) `REAL300000237173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237173 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 110, 110, 110, 110, 110, 168, 110, 110, 144, 144, 110, 30, 30, 11, 1, 11, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 162, 162, 162, 110, 168, 168, 168, 110, 30, 30, 1, 1, 1, 3, 3, 1] 201 rigid atoms, others: [38, 39, 40, 43, 15, 17, 18, 19, 20, 21, 22, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42]) total number of confs: 532 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237173 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 114, 114, 114, 114, 114, 172, 114, 114, 147, 147, 114, 45, 45, 19, 3, 19, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 166, 166, 166, 114, 172, 172, 172, 114, 45, 45, 3, 3, 3, 1, 1, 3] 201 rigid atoms, others: [41, 42, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 567 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: REAL300000237173 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 3, 3, 1, 1, 1, 9, 9, 39, 39, 110, 110, 110, 110, 110, 112, 112, 112, 112, 110, 4, 4, 4, 1, 3, 3, 3, 1, 9, 9, 110, 110, 110, 112, 112, 110] 201 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 11, 12, 13, 35, 31] set([0, 6, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 212 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237173 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237173 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237173/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237173 Building REAL300000237174 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237174' /scratch/stefan/7769818/working/building/REAL300000237174 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237174 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237174/0 /scratch/stefan/7769818/working/building/REAL300000237174 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/174 `/scratch/stefan/7769818/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1F) `REAL300000237174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237174 none O=C([O-])C1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 193, 193, 83, 83, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 193, 193, 193, 193, 193, 83, 83, 1, 1, 1, 6, 6, 1, 193, 193] 201 rigid atoms, others: [33, 8, 10, 11, 12, 13, 14, 15, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 34, 35]) total number of confs: 404 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237174 none O=C([O-])C1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 153, 153, 40, 7, 40, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 7, 201, 201, 201, 201, 201, 153, 153, 6, 7, 7, 1, 1, 7, 201, 201] 201 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 462 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: REAL300000237174 none O=C([O-])C1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 5, 5, 44, 44, 193, 193, 193, 193, 193, 201, 201, 201, 201, 193, 1, 1, 1, 1, 1, 5, 5, 193, 193, 193, 201, 201, 193, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 304 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237174 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237174 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237174/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237174 Building REAL300000237175 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237175' /scratch/stefan/7769818/working/building/REAL300000237175 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237175 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237175/0 /scratch/stefan/7769818/working/building/REAL300000237175 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/175 `/scratch/stefan/7769818/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1) `REAL300000237175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237175 none O=C([O-])CC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 115, 76, 158, 158, 76, 76, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 158, 158, 158, 158, 158, 158, 76, 76, 1, 1, 1, 6, 6, 1, 158, 158] 158 rigid atoms, others: [32, 33, 36, 10, 12, 13, 14, 15, 16, 17, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 37, 38]) total number of confs: 818 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237175 none O=C([O-])CC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 132, 113, 157, 157, 113, 113, 42, 9, 42, 9, 8, 9, 9, 1, 1, 1, 1, 1, 1, 9, 157, 157, 157, 157, 157, 157, 113, 113, 8, 9, 9, 1, 1, 9, 157, 157] 157 rigid atoms, others: [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, 33, 36, 37, 38]) total number of confs: 646 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: REAL300000237175 none O=C([O-])CC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 5, 5, 46, 46, 158, 158, 158, 158, 158, 158, 158, 158, 158, 158, 1, 1, 2, 2, 1, 1, 5, 5, 158, 158, 158, 158, 158, 158, 1, 1] 158 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: 262 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237175 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237175 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237175/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237175 Building REAL300000237176 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237176' /scratch/stefan/7769818/working/building/REAL300000237176 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237176 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237176/0 /scratch/stefan/7769818/working/building/REAL300000237176 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/176 `/scratch/stefan/7769818/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(Br)=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1) `REAL300000237176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237176 none O=C([O-])C1=CC(Br)=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.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, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [192, 191, 192, 191, 191, 191, 191, 191, 93, 93, 12, 1, 12, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 191, 191, 191, 93, 93, 1, 1, 1, 4, 4, 1, 191] 192 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 32, 33, 35]) total number of confs: 376 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237176 none O=C([O-])C1=CC(Br)=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.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, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 192, 192, 192, 192, 192, 192, 141, 141, 40, 7, 40, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 7, 192, 192, 192, 141, 141, 6, 7, 7, 1, 1, 7, 192] 192 rigid atoms, others: [32, 33, 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, 34, 35]) total number of confs: 440 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: REAL300000237176 none O=C([O-])C1=CC(Br)=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.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, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 43, 43, 191, 191, 191, 191, 191, 192, 192, 192, 192, 191, 1, 1, 1, 6, 6, 191, 191, 191, 192, 192, 191, 1] 192 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 35, 24, 25, 26] 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]) total number of confs: 287 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237176 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237176 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237176/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237176 Building REAL300000237177 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237177' /scratch/stefan/7769818/working/building/REAL300000237177 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237177 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237177/0 /scratch/stefan/7769818/working/building/REAL300000237177 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/177 `/scratch/stefan/7769818/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)S1) `REAL300000237177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237177 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 14, 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, 7, 7, 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, 142, 60, 60, 13, 1, 13, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 142, 142, 142, 60, 60, 1, 1, 1, 3, 3, 1] 142 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16, 21, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 263 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237177 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 140, 140, 140, 140, 79, 79, 33, 6, 33, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 140, 140, 140, 79, 79, 6, 6, 6, 1, 1, 6] 140 rigid atoms, others: [15, 16, 17, 18, 19, 20, 30, 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, 32]) total number of confs: 288 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: REAL300000237177 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 12, 79, 79, 142, 142, 142, 142, 142, 142, 142, 142, 142, 142, 1, 1, 1, 12, 12, 142, 142, 142, 142, 142, 142] 142 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]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237177 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237177 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237177/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237177 Building REAL300000237178 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237178' /scratch/stefan/7769818/working/building/REAL300000237178 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237178 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237178/0 /scratch/stefan/7769818/working/building/REAL300000237178 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/178 `/scratch/stefan/7769818/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1) `REAL300000237178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237178 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 200, 201, 171, 201, 201, 95, 95, 12, 1, 12, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 201, 201, 201, 201, 201, 201, 95, 95, 1, 1, 1, 4, 4, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 37, 11, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 38, 39]) total number of confs: 545 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237178 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 162, 164, 144, 164, 164, 105, 105, 40, 9, 40, 9, 8, 9, 9, 1, 1, 1, 1, 1, 1, 9, 164, 164, 164, 164, 164, 164, 105, 105, 8, 9, 9, 1, 1, 9, 164, 164] 164 rigid atoms, others: [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, 34, 37, 38, 39]) total number of confs: 459 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: REAL300000237178 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 14, 4, 1, 1, 1, 1, 1, 1, 5, 5, 45, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 4, 4, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 24, 25, 38, 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]) total number of confs: 328 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237178 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237178 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237178/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237178 Building REAL300000237179 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237179' /scratch/stefan/7769818/working/building/REAL300000237179 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237179 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237179/0 /scratch/stefan/7769818/working/building/REAL300000237179 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/179 `/scratch/stefan/7769818/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C(F)=C1) `REAL300000237179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237179 none O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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, 67, 67, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 201, 201, 201, 201, 67, 67, 1, 1, 1, 3, 3, 1, 201] 201 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 35]) total number of confs: 344 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237179 none O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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, 100, 100, 33, 4, 33, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 201, 201, 201, 201, 101, 100, 4, 4, 4, 1, 1, 4, 201] 201 rigid atoms, others: [32, 33, 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, 34, 35]) total number of confs: 404 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: REAL300000237179 none O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 77, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 11, 11, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26] set([0, 2, 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: 354 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237179 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237179 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237179/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237179 Building REAL300000237180 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237180' /scratch/stefan/7769818/working/building/REAL300000237180 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237180 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237180/0 /scratch/stefan/7769818/working/building/REAL300000237180 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/180 `/scratch/stefan/7769818/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NNC2=CC=CC(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)=C21) `REAL300000237180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237180 none O=C([O-])C1=NNC2=CC=CC(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 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, 31, 31, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 41, 41, 41, 41, 41, 31, 31, 1, 1, 1, 3, 3, 1] 41 rigid atoms, others: [33, 34, 35, 38, 13, 15, 16, 17, 18, 19, 20, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237180 none O=C([O-])C1=NNC2=CC=CC(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 73, 73, 40, 6, 41, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 88, 88, 88, 88, 88, 73, 73, 6, 6, 6, 1, 1, 6] 88 rigid atoms, others: [36, 37, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 212 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: REAL300000237180 none O=C([O-])C1=NNC2=CC=CC(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 7, 7, 41, 41, 41, 41, 41, 41] 41 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29, 30] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237180 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237180 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237180/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237180 Building REAL300000237181 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237181' /scratch/stefan/7769818/working/building/REAL300000237181 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237181 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237181/0 /scratch/stefan/7769818/working/building/REAL300000237181 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/181 `/scratch/stefan/7769818/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C(C2=CC=CC=C2)=N1) `REAL300000237181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237181 none O=C([O-])CN1C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7] dock color type numbers: [2, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 26, 6, 6, 6, 6, 6, 20, 20, 55, 55, 156, 156, 156, 156, 156, 158, 158, 158, 158, 156, 1, 1, 1, 1, 1, 1, 1, 6, 16, 16, 6, 20, 20, 156, 156, 156, 158, 158, 156, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 351 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237181 none O=C([O-])CN1C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7] dock color type numbers: [2, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 194, 194, 112, 112, 112, 35, 35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 112, 112, 156, 156, 112, 156, 156, 112, 194, 194, 112, 35, 35, 1, 1, 1, 3, 3, 1, 156, 156, 113, 156, 156] 201 rigid atoms, others: [35, 36, 37, 40, 9, 11, 12, 13, 14, 15, 16, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 809 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237181 none O=C([O-])CN1C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7] dock color type numbers: [2, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 194, 194, 138, 138, 138, 56, 56, 25, 5, 26, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 138, 138, 174, 174, 138, 174, 174, 138, 194, 194, 138, 56, 55, 4, 4, 4, 1, 1, 4, 174, 174, 139, 174, 174] 201 rigid atoms, others: [38, 39, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 743 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: REAL300000237181 none O=C([O-])CN1C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7] dock color type numbers: [2, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 10, 1, 1, 1, 1, 1, 10, 10, 31, 32, 112, 112, 112, 112, 112, 120, 120, 120, 120, 112, 1, 1, 6, 6, 1, 6, 6, 1, 6, 6, 1, 10, 10, 112, 112, 112, 120, 120, 112, 6, 6, 1, 6, 6] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 22, 23, 29] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237181 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237181 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237181/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237181 Building REAL300000237182 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237182' /scratch/stefan/7769818/working/building/REAL300000237182 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237182 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237182/0 /scratch/stefan/7769818/working/building/REAL300000237182 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/182 `/scratch/stefan/7769818/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C=C2)C=C1) `REAL300000237182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237182 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.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, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 88, 113, 88, 113, 113, 88, 82, 88, 88, 82, 82, 35, 7, 35, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 7, 88, 88, 113, 113, 113, 113, 88, 88, 82, 82, 6, 7, 7, 1, 1, 7, 88, 88, 113, 113] 113 rigid atoms, others: [39, 40, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 484 number of broken/clashed sets: 10 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237182 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.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, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 26, 26, 74, 74, 74, 74, 74, 85, 85, 85, 85, 74, 1, 1, 3, 3, 3, 3, 1, 1, 4, 4, 74, 74, 74, 85, 85, 74, 1, 1, 3, 3] 115 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 43, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 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, 44, 45]) total number of confs: 161 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237182 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.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, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 77, 113, 77, 113, 113, 77, 68, 77, 77, 67, 67, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 77, 77, 113, 113, 113, 113, 77, 77, 67, 67, 1, 1, 1, 6, 6, 1, 77, 77, 113, 113] 113 rigid atoms, others: [36, 37, 38, 41, 13, 15, 16, 17, 18, 19, 20, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 42, 43, 44, 45]) total number of confs: 554 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: REAL300000237182 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.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, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 43, 43, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 3, 3, 1, 1, 1, 1, 3, 3, 8, 8, 115, 115, 115, 115, 115, 115, 3, 3, 1, 1] 115 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 45, 28, 29, 30, 31] set([0, 2, 8, 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, 42, 43]) total number of confs: 211 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237182 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237182 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237182/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237182 Building REAL300000237183 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237183' /scratch/stefan/7769818/working/building/REAL300000237183 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237183 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237183/0 /scratch/stefan/7769818/working/building/REAL300000237183 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/183 `/scratch/stefan/7769818/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2NC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C2=C1) `REAL300000237183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237183 none O=C([O-])C1=CC=C2NC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 60, 60, 12, 1, 12, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 201, 201, 201, 201, 201, 201, 60, 60, 1, 1, 1, 5, 5, 1, 201] 201 rigid atoms, others: [33, 34, 35, 38, 12, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 39]) total number of confs: 339 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237183 none O=C([O-])C1=CC=C2NC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 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 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 74, 74, 74, 74, 74, 74, 55, 55, 28, 7, 28, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 74, 74, 74, 74, 74, 74, 55, 55, 6, 6, 7, 1, 1, 7, 74] 74 rigid atoms, others: [36, 37, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 184 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: REAL300000237183 none O=C([O-])C1=CC=C2NC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 74, 75, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 11, 11, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 25, 26, 27, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237183 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237183 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237183/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237183 Building REAL300000237184 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237184' /scratch/stefan/7769818/working/building/REAL300000237184 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237184 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237184/0 /scratch/stefan/7769818/working/building/REAL300000237184 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/184 `/scratch/stefan/7769818/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=N1) `REAL300000237184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237184 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 117, 117, 117, 76, 76, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 117, 117, 117, 117, 76, 76, 1, 1, 1, 5, 5, 1, 117] 117 rigid atoms, others: [33, 9, 11, 12, 13, 14, 15, 16, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 32, 34]) total number of confs: 261 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237184 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 117, 117, 117, 91, 91, 30, 6, 30, 6, 5, 6, 6, 1, 1, 1, 1, 1, 1, 6, 117, 117, 117, 117, 91, 91, 5, 6, 6, 1, 1, 6, 117] 117 rigid atoms, others: [32, 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, 33, 34]) total number of confs: 272 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: REAL300000237184 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 41, 41, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 1, 1, 1, 1, 5, 5, 117, 117, 117, 117, 117, 117, 1] 117 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 203 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237184 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237184 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237184/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237184 Building REAL300000237185 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237185' /scratch/stefan/7769818/working/building/REAL300000237185 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237185 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237185/0 /scratch/stefan/7769818/working/building/REAL300000237185 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/185 `/scratch/stefan/7769818/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1O) `REAL300000237185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237185 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 192, 201, 192, 192, 192, 83, 83, 12, 1, 12, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 192, 192, 192, 192, 192, 83, 83, 1, 1, 1, 4, 4, 1, 192, 384] 402 rigid atoms, others: [34, 9, 11, 12, 13, 14, 15, 16, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 35, 36]) total number of confs: 778 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237185 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 388 conformations in input total number of sets (complete confs): 388 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 193, 193, 193, 143, 143, 46, 7, 47, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 194, 194, 194, 193, 193, 143, 142, 7, 7, 7, 1, 1, 7, 194, 388] 388 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 851 number of broken/clashed sets: 6 ./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: REAL300000237185 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 48, 48, 192, 192, 192, 192, 192, 200, 200, 200, 200, 192, 1, 1, 1, 1, 1, 5, 5, 192, 192, 192, 200, 200, 192, 1, 2] 402 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25, 26] 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, 36]) total number of confs: 319 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237185 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237185 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237185/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237185 Building REAL300000237186 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237186' /scratch/stefan/7769818/working/building/REAL300000237186 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237186 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237186/0 /scratch/stefan/7769818/working/building/REAL300000237186 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/186 `/scratch/stefan/7769818/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1C(=O)[O-]) `REAL300000237186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237186 none CC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 200, 200, 87, 87, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 200, 200, 200, 201, 201, 200, 200, 200, 200, 200, 87, 87, 1, 1, 1, 4, 4, 1, 200] 201 rigid atoms, others: [32, 33, 34, 37, 7, 9, 10, 11, 12, 13, 14, 19] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 38]) total number of confs: 385 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237186 none CC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 3, 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 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, 147, 147, 36, 7, 36, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 147, 147, 6, 7, 7, 1, 1, 7, 201] 201 rigid atoms, others: [35, 36, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 450 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: REAL300000237186 none CC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 3, 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 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, 6, 6, 44, 44, 200, 200, 200, 200, 200, 201, 201, 201, 201, 200, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 6, 6, 200, 200, 200, 201, 201, 200, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 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]) total number of confs: 306 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237186 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237186 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237186/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237186 Building REAL300000237187 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237187' /scratch/stefan/7769818/working/building/REAL300000237187 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237187 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237187/0 /scratch/stefan/7769818/working/building/REAL300000237187 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/187 `/scratch/stefan/7769818/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)SC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1) `REAL300000237187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237187 none O=C([O-])C1=C(Cl)SC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 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: [201, 201, 201, 201, 201, 201, 201, 48, 48, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 201, 48, 48, 1, 1, 1, 3, 3, 1, 201] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 22, 26, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 11, 18, 19, 20, 21, 23, 24, 25, 29, 30]) total number of confs: 308 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237187 none O=C([O-])C1=C(Cl)SC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 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: [201, 201, 201, 201, 201, 201, 201, 74, 74, 29, 5, 29, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 201, 74, 73, 4, 5, 5, 1, 1, 5, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 365 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: REAL300000237187 none O=C([O-])C1=C(Cl)SC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 88, 89, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 13, 13, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 23] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237187 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237187 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237187/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237187 Building REAL300000237188 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237188' /scratch/stefan/7769818/working/building/REAL300000237188 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237188 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237188/0 /scratch/stefan/7769818/working/building/REAL300000237188 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/188 `/scratch/stefan/7769818/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)O1) `REAL300000237188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237188 none CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 188, 188, 188, 188, 188, 85, 85, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 187, 188, 188, 188, 188, 85, 85, 1, 1, 1, 6, 6, 1] 188 rigid atoms, others: [32, 35, 10, 12, 13, 14, 15, 16, 17, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 356 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237188 none CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 132, 132, 36, 7, 36, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 201, 201, 201, 201, 201, 132, 132, 6, 7, 7, 1, 1, 6] 201 rigid atoms, others: [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, 32, 35]) total number of confs: 439 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: REAL300000237188 none CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 1, 1, 1, 12, 12, 66, 66, 188, 188, 188, 188, 188, 188, 188, 188, 188, 188, 1, 2, 2, 2, 1, 12, 12, 188, 188, 188, 188, 188, 188] 188 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 23, 27] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237188 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237188 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237188/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237188 Building REAL300000237189 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237189' /scratch/stefan/7769818/working/building/REAL300000237189 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237189 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237189/0 /scratch/stefan/7769818/working/building/REAL300000237189 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/189 `/scratch/stefan/7769818/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1) `REAL300000237189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237189 none CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 137, 137, 137, 137, 137, 68, 68, 12, 1, 12, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 137, 137, 137, 137, 68, 68, 1, 1, 1, 5, 5, 1] 137 rigid atoms, others: [32, 35, 11, 13, 14, 15, 16, 17, 18, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237189 none CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 127, 127, 127, 127, 86, 86, 36, 5, 36, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 127, 127, 127, 127, 86, 86, 4, 5, 5, 1, 1, 5] 127 rigid atoms, others: [33, 34, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 293 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: REAL300000237189 none CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 65, 65, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 2, 2, 2, 1, 10, 10, 137, 137, 137, 137, 137, 137] 137 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237189 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237189 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237189/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237189 Building REAL300000237190 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237190' /scratch/stefan/7769818/working/building/REAL300000237190 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237190 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237190/0 /scratch/stefan/7769818/working/building/REAL300000237190 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/190 `/scratch/stefan/7769818/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1) `REAL300000237190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237190 none O=C([O-])C1=CN=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.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, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 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 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 133, 132, 133, 133, 68, 68, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 133, 132, 133, 68, 68, 1, 1, 1, 6, 6, 1, 133] 133 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17, 22, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 34]) total number of confs: 276 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237190 none O=C([O-])C1=CN=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.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, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 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 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 133, 133, 133, 133, 101, 101, 39, 8, 39, 8, 7, 8, 8, 1, 1, 1, 1, 1, 1, 8, 133, 133, 133, 101, 101, 7, 8, 8, 1, 1, 8, 133] 133 rigid atoms, others: [32, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 306 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: REAL300000237190 none O=C([O-])C1=CN=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.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, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 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 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 44, 45, 133, 133, 133, 133, 133, 133, 133, 133, 133, 133, 1, 1, 1, 7, 7, 133, 133, 133, 133, 133, 133, 1] 133 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 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]) total number of confs: 217 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237190 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237190 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237190/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237190 Building REAL300000237191 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237191' /scratch/stefan/7769818/working/building/REAL300000237191 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237191 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237191/0 /scratch/stefan/7769818/working/building/REAL300000237191 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/191 `/scratch/stefan/7769818/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=COC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1) `REAL300000237191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237191 none O=C([O-])C1=COC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [150, 150, 150, 150, 150, 150, 74, 74, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 150, 150, 74, 74, 1, 1, 1, 6, 6, 1, 150] 150 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 21, 26, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 32, 22, 23, 24, 25, 29, 30]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237191 none O=C([O-])C1=COC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [150, 150, 150, 150, 150, 150, 98, 98, 38, 7, 38, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 7, 150, 150, 98, 98, 6, 7, 7, 1, 1, 7, 150] 150 rigid atoms, others: [15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 339 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: REAL300000237191 none O=C([O-])C1=COC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 75, 76, 150, 150, 150, 150, 150, 150, 150, 150, 150, 150, 1, 1, 13, 13, 150, 150, 150, 150, 150, 150, 1] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 22, 23] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237191 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237191 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237191/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237191 Building REAL300000237192 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237192' /scratch/stefan/7769818/working/building/REAL300000237192 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237192 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237192/0 /scratch/stefan/7769818/working/building/REAL300000237192 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/192 `/scratch/stefan/7769818/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1) `REAL300000237192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237192 none COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 194, 194, 194, 194, 194, 194, 194, 194, 194, 54, 54, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 201, 201, 201, 194, 194, 194, 54, 54, 1, 1, 1, 3, 3, 1] 201 rigid atoms, others: [34, 35, 36, 39, 13, 15, 16, 17, 18, 19, 20, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 330 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237192 none COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 97, 97, 33, 6, 34, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 201, 201, 201, 201, 201, 201, 97, 97, 6, 6, 6, 1, 1, 6] 201 rigid atoms, others: [37, 38, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 397 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: REAL300000237192 none COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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, 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, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 9, 9, 68, 68, 194, 194, 194, 194, 194, 201, 201, 201, 201, 194, 4, 4, 4, 1, 1, 1, 9, 9, 194, 194, 194, 201, 201, 194] 201 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]) total number of confs: 345 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237192 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237192 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237192/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237192 Building REAL300000237193 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237193' /scratch/stefan/7769818/working/building/REAL300000237193 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237193 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237193/0 /scratch/stefan/7769818/working/building/REAL300000237193 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/193 `/scratch/stefan/7769818/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2SC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C2=C1) `REAL300000237193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237193 none O=C([O-])C1=CC=C2SC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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, 7, 7, 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 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [183, 183, 183, 183, 183, 183, 183, 183, 183, 69, 69, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 183, 183, 183, 183, 183, 69, 69, 1, 1, 1, 3, 3, 1, 183] 183 rigid atoms, others: [32, 33, 34, 37, 12, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 38]) total number of confs: 316 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237193 none O=C([O-])C1=CC=C2SC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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, 7, 7, 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 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, 45, 45, 23, 6, 23, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 1, 1, 5, 45] 45 rigid atoms, others: [35, 36, 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, 37, 38]) total number of confs: 124 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: REAL300000237193 none O=C([O-])C1=CC=C2SC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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, 7, 7, 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 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 60, 60, 183, 183, 183, 183, 183, 183, 183, 183, 183, 183, 1, 1, 1, 1, 1, 9, 9, 183, 183, 183, 183, 183, 183, 1] 183 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 38, 25, 26, 27, 28, 29] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237193 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237193 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237193/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237193 Building REAL300000237194 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237194' /scratch/stefan/7769818/working/building/REAL300000237194 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237194 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237194/0 /scratch/stefan/7769818/working/building/REAL300000237194 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/194 `/scratch/stefan/7769818/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Br)C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1) `REAL300000237194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237194 none O=C([O-])C1=CC=C(Br)C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.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, 1, 1, 1, 1, 17, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 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, 201, 201, 201, 201, 201, 87, 87, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 201, 201, 201, 87, 87, 1, 1, 1, 5, 5, 1, 201] 201 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 32, 33, 35]) total number of confs: 379 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237194 none O=C([O-])C1=CC=C(Br)C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.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, 1, 1, 1, 1, 17, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 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 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 197, 197, 197, 197, 197, 140, 140, 48, 8, 48, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 197, 197, 197, 140, 140, 8, 8, 8, 1, 1, 8, 197] 197 rigid atoms, others: [32, 33, 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, 34, 35]) total number of confs: 442 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: REAL300000237194 none O=C([O-])C1=CC=C(Br)C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.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, 1, 1, 1, 1, 17, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 60, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 9, 9, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 24, 25, 26] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 322 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237194 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237194 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237194/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237194 Building REAL300000237195 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237195' /scratch/stefan/7769818/working/building/REAL300000237195 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237195 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237195/0 /scratch/stefan/7769818/working/building/REAL300000237195 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/195 `/scratch/stefan/7769818/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C([N+](=O)[O-])=C1) `REAL300000237195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237195 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 8, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 93, 174, 93, 174, 174, 93, 93, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 174, 174, 174, 174, 174, 174, 174, 93, 93, 1, 1, 1, 3, 3, 1, 174] 174 rigid atoms, others: [32, 33, 36, 9, 11, 12, 13, 14, 15, 16, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 37]) total number of confs: 848 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237195 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 8, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 140, 174, 140, 174, 174, 140, 140, 50, 7, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 174, 174, 174, 174, 174, 174, 174, 140, 139, 6, 7, 6, 1, 1, 6, 174] 174 rigid atoms, others: [34, 35, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 659 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: REAL300000237195 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 8, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 43, 43, 174, 174, 174, 174, 174, 174, 174, 174, 174, 174, 1, 1, 2, 2, 1, 1, 1, 5, 5, 174, 174, 174, 174, 174, 174, 1] 174 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 26, 27, 28, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237195 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237195 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237195/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237195 Building REAL300000237196 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237196' /scratch/stefan/7769818/working/building/REAL300000237196 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237196 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237196/0 /scratch/stefan/7769818/working/building/REAL300000237196 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/196 `/scratch/stefan/7769818/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1) `REAL300000237196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237196 none O=C([O-])CC1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 137, 137, 106, 137, 137, 63, 63, 12, 1, 12, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 137, 201, 201, 137, 137, 137, 63, 63, 1, 1, 1, 4, 4, 1, 137] 201 rigid atoms, others: [32, 33, 34, 37, 11, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 38]) total number of confs: 807 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237196 none O=C([O-])CC1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 156, 156, 124, 156, 156, 99, 99, 34, 7, 34, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 7, 156, 201, 201, 156, 156, 156, 99, 99, 6, 7, 7, 1, 1, 7, 156] 201 rigid atoms, others: [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, 34, 37, 38]) total number of confs: 776 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: REAL300000237196 none O=C([O-])CC1=CC=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 41, 41, 137, 137, 137, 137, 137, 142, 142, 142, 142, 137, 1, 2, 2, 1, 1, 1, 5, 5, 137, 137, 137, 142, 142, 137, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 38, 24, 27, 28, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 247 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237196 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237196 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237196/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237196 Building REAL300000237197 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237197' /scratch/stefan/7769818/working/building/REAL300000237197 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237197 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237197/0 /scratch/stefan/7769818/working/building/REAL300000237197 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/197 `/scratch/stefan/7769818/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1C(=O)[O-]) `REAL300000237197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237197 none COC1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 154, 154, 154, 59, 59, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 154, 154, 154, 154, 199, 199, 201, 201, 201, 154, 59, 59, 1, 1, 1, 3, 3, 1, 154, 154] 201 rigid atoms, others: [32, 33, 34, 37, 7, 9, 10, 11, 12, 13, 14, 19] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 38, 39]) total number of confs: 564 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237197 none COC1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 166, 166, 166, 76, 76, 30, 4, 31, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 166, 166, 166, 166, 201, 201, 201, 201, 201, 166, 76, 76, 4, 4, 4, 1, 1, 4, 166, 166] 201 rigid atoms, others: [35, 36, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 539 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: REAL300000237197 none COC1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 3, 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 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, 42, 42, 154, 154, 154, 154, 154, 164, 164, 164, 164, 154, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 5, 5, 154, 154, 154, 164, 164, 154, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 20, 21, 22, 23, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 267 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237197 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237197 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237197/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237197 Building REAL300000237198 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237198' /scratch/stefan/7769818/working/building/REAL300000237198 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237198 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237198/0 /scratch/stefan/7769818/working/building/REAL300000237198 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/198 `/scratch/stefan/7769818/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C(F)=C1) `REAL300000237198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237198 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 86, 125, 85, 125, 125, 125, 85, 85, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 125, 125, 125, 125, 85, 85, 1, 1, 1, 6, 6, 1, 125] 125 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 35]) total number of confs: 529 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237198 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 109, 125, 109, 125, 125, 125, 109, 109, 41, 9, 41, 9, 8, 9, 9, 1, 1, 1, 1, 1, 1, 9, 125, 125, 125, 125, 109, 109, 8, 9, 9, 1, 1, 9, 125] 125 rigid atoms, others: [32, 33, 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, 34, 35]) total number of confs: 429 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: REAL300000237198 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 124, 124, 124, 124, 124, 124, 124, 124, 124, 124, 1, 1, 1, 1, 7, 7, 124, 124, 124, 124, 124, 124, 1] 124 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26] set([0, 2, 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: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237198 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237198 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237198/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237198 Building REAL300000237199 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237199' /scratch/stefan/7769818/working/building/REAL300000237199 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237199 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237199/0 /scratch/stefan/7769818/working/building/REAL300000237199 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/199 `/scratch/stefan/7769818/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C(F)C=C1) `REAL300000237199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237199 none O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 60, 60, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 201, 201, 201, 201, 60, 60, 1, 1, 1, 3, 3, 1, 201, 201] 201 rigid atoms, others: [33, 9, 11, 12, 13, 14, 15, 16, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 32, 34, 35]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237199 none O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 106, 106, 33, 6, 33, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 201, 201, 201, 201, 106, 105, 6, 6, 6, 1, 1, 6, 201, 201] 201 rigid atoms, others: [32, 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, 33, 34, 35]) total number of confs: 395 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: REAL300000237199 none O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 11, 11, 70, 70, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 11, 11, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237199 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237199 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237199/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237199 Building REAL300000237200 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237200' /scratch/stefan/7769818/working/building/REAL300000237200 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237200 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237200/0 /scratch/stefan/7769818/working/building/REAL300000237200 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/200 `/scratch/stefan/7769818/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CS1) `REAL300000237200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237200 none O=C([O-])C1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 75, 75, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 131, 131, 131, 75, 75, 1, 1, 1, 6, 6, 1, 131] 131 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 20, 26, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 32, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237200 none O=C([O-])C1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 116, 116, 46, 9, 46, 9, 8, 9, 9, 1, 1, 1, 1, 1, 1, 9, 131, 131, 131, 116, 116, 8, 9, 9, 1, 1, 9, 131] 131 rigid atoms, others: [14, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 324 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: REAL300000237200 none O=C([O-])C1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 2, 1, 1, 1, 1, 7, 7, 43, 44, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 1, 1, 1, 7, 7, 131, 131, 131, 131, 131, 131, 1] 131 rigid atoms, others: [32, 1, 3, 4, 5, 6, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237200 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237200 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237200/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237200 Building REAL300000237201 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237201' /scratch/stefan/7769818/working/building/REAL300000237201 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237201 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237201/0 /scratch/stefan/7769818/working/building/REAL300000237201 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/201 `/scratch/stefan/7769818/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1OCC(=O)[O-]) `REAL300000237201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237201 none CCOC1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 79, 44, 44, 44, 13, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 151, 197, 199, 199, 85, 85, 85, 85, 85, 44, 13, 13, 1, 1, 1, 2, 2, 1, 44, 44, 197, 197] 201 rigid atoms, others: [37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 43, 44, 45, 46]) total number of confs: 597 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237201 none CCOC1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 87, 53, 53, 53, 24, 24, 15, 3, 15, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 53, 53, 53, 53, 149, 195, 199, 199, 97, 97, 97, 97, 97, 53, 24, 24, 2, 3, 3, 1, 1, 3, 53, 53, 195, 195] 201 rigid atoms, others: [40, 41, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46]) total number of confs: 638 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: REAL300000237201 none CCOC1=CC(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 5, 5, 13, 13, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 7, 21, 31, 31, 5, 5, 5, 5, 5, 1, 5, 5, 44, 44, 44, 44, 44, 44, 1, 1, 21, 21] 201 rigid atoms, others: [34, 3, 4, 5, 6, 43, 44, 2, 21, 22, 23, 24] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237201 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237201 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237201/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237201 Building REAL300000237202 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237202' /scratch/stefan/7769818/working/building/REAL300000237202 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237202 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237202/0 /scratch/stefan/7769818/working/building/REAL300000237202 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/202 `/scratch/stefan/7769818/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1F) `REAL300000237202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237202 none O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [124, 117, 124, 116, 117, 117, 117, 92, 92, 12, 1, 12, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 117, 117, 117, 117, 92, 92, 1, 1, 1, 4, 4, 1, 117] 124 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 35]) total number of confs: 296 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237202 none O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 123, 124, 124, 124, 110, 110, 38, 7, 38, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 7, 124, 124, 124, 124, 110, 110, 6, 7, 7, 1, 1, 7, 124] 124 rigid atoms, others: [32, 33, 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, 34, 35]) total number of confs: 312 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: REAL300000237202 none O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 24, 24, 117, 117, 117, 117, 117, 124, 124, 124, 124, 117, 1, 1, 1, 1, 3, 3, 117, 117, 117, 124, 124, 117, 1] 124 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26] set([0, 2, 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: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237202 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237202 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237202/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237202 Building REAL300000237203 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237203' /scratch/stefan/7769818/working/building/REAL300000237203 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237203 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237203/0 /scratch/stefan/7769818/working/building/REAL300000237203 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/203 `/scratch/stefan/7769818/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)O2)N1) `REAL300000237203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237203 none O=C([O-])C1=CC2=C(C=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)O2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 122, 122, 122, 122, 122, 122, 67, 67, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 122, 122, 122, 122, 67, 67, 1, 1, 1, 4, 3, 1, 122] 122 rigid atoms, others: [32, 35, 11, 13, 14, 15, 16, 17, 18, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 36]) total number of confs: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237203 none O=C([O-])C1=CC2=C(C=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)O2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 122, 122, 122, 122, 122, 122, 81, 81, 25, 5, 25, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 122, 122, 122, 122, 81, 81, 4, 5, 5, 1, 1, 4, 122] 122 rigid atoms, others: [33, 34, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 271 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: REAL300000237203 none O=C([O-])C1=CC2=C(C=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)O2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 60, 60, 122, 122, 122, 122, 122, 122, 122, 122, 122, 122, 1, 1, 1, 1, 11, 11, 122, 122, 122, 122, 122, 122, 1] 122 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 36] set([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: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237203 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237203 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237203/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237203 Building REAL300000237204 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237204' /scratch/stefan/7769818/working/building/REAL300000237204 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237204 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237204/0 /scratch/stefan/7769818/working/building/REAL300000237204 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/204 `/scratch/stefan/7769818/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)=CC=C2O1) `REAL300000237204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237204 none O=C([O-])C1=CC2=CC(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 139, 139, 139, 139, 78, 78, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 139, 139, 139, 139, 139, 139, 78, 78, 1, 1, 1, 6, 6, 1, 139, 139] 139 rigid atoms, others: [32, 33, 36, 10, 12, 13, 14, 15, 16, 17, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 37, 38]) total number of confs: 287 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237204 none O=C([O-])C1=CC2=CC(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 139, 139, 139, 139, 98, 98, 36, 9, 36, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 139, 139, 139, 139, 139, 139, 98, 98, 8, 9, 9, 1, 1, 9, 139, 139] 139 rigid atoms, others: [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, 33, 36, 37, 38]) total number of confs: 318 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: REAL300000237204 none O=C([O-])C1=CC2=CC(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 40, 40, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 1, 1, 1, 1, 1, 1, 6, 6, 139, 139, 139, 139, 139, 139, 1, 1] 139 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 38, 23, 24, 25, 26, 27, 28, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 224 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237204 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237204 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237204/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237204 Building REAL300000237205 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237205' /scratch/stefan/7769818/working/building/REAL300000237205 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237205 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237205/0 /scratch/stefan/7769818/working/building/REAL300000237205 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/205 `/scratch/stefan/7769818/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)=CC=CN12) `REAL300000237205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237205 none O=C([O-])C1=CN=C2C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 73, 73, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 201, 201, 201, 201, 201, 73, 73, 1, 1, 1, 5, 5, 1, 201, 201, 201] 201 rigid atoms, others: [32, 35, 10, 12, 13, 14, 15, 16, 17, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 36, 37, 38]) total number of confs: 345 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237205 none O=C([O-])C1=CN=C2C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 141, 141, 141, 141, 141, 97, 97, 44, 7, 45, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 141, 141, 141, 141, 141, 97, 97, 6, 6, 6, 1, 1, 6, 141, 141, 141] 141 rigid atoms, others: [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, 32, 35, 36, 37, 38]) total number of confs: 317 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: REAL300000237205 none O=C([O-])C1=CN=C2C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 84, 84, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 11, 11, 201, 201, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 25, 23, 24, 36, 26, 27, 37] set([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: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237205 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237205 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237205/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237205 Building REAL300000237206 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237206' /scratch/stefan/7769818/working/building/REAL300000237206 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237206 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237206/0 /scratch/stefan/7769818/working/building/REAL300000237206 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/206 `/scratch/stefan/7769818/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1) `REAL300000237206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237206 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 73, 73, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 201, 201, 201, 201, 201, 201, 201, 73, 73, 1, 1, 1, 3, 3, 1] 201 rigid atoms, others: [38, 39, 40, 43, 16, 18, 19, 20, 21, 22, 23, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42]) total number of confs: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237206 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 109, 109, 37, 7, 37, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 201, 201, 201, 201, 201, 201, 201, 109, 109, 6, 6, 6, 1, 1, 6] 201 rigid atoms, others: [41, 42, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 411 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: REAL300000237206 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.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, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 73, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 9, 9, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 34, 35] set([4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237206 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237206 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237206/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237206 Building REAL300000237207 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237207' /scratch/stefan/7769818/working/building/REAL300000237207 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237207 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237207/0 /scratch/stefan/7769818/working/building/REAL300000237207 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/207 `/scratch/stefan/7769818/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN2C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)=CN=C2C=C1) `REAL300000237207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237207 none O=C([O-])C1=CN2C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 72, 72, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 201, 201, 201, 201, 201, 201, 72, 72, 1, 1, 1, 3, 3, 1, 201, 201, 201] 201 rigid atoms, others: [32, 35, 9, 11, 12, 13, 14, 15, 16, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 36, 37, 38]) total number of confs: 339 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237207 none O=C([O-])C1=CN2C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 104, 104, 104, 69, 69, 30, 6, 30, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 104, 104, 104, 104, 104, 104, 69, 69, 6, 6, 6, 1, 1, 6, 104, 104, 104] 104 rigid atoms, others: [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, 32, 35, 36, 37, 38]) total number of confs: 239 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: REAL300000237207 none O=C([O-])C1=CN2C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 72, 72, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 11, 11, 201, 201, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 25, 22, 23, 24, 36, 26, 27, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237207 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237207 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237207/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237207 Building REAL300000237208 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237208' /scratch/stefan/7769818/working/building/REAL300000237208 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237208 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237208/0 /scratch/stefan/7769818/working/building/REAL300000237208 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/208 `/scratch/stefan/7769818/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C=C2)C=N1) `REAL300000237208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237208 none O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 123, 123, 198, 198, 123, 123, 37, 8, 37, 8, 7, 8, 8, 1, 1, 1, 1, 1, 1, 8, 198, 198, 201, 201, 201, 198, 198, 123, 123, 7, 8, 8, 1, 1, 8, 198, 198, 201] 201 rigid atoms, others: [37, 38, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 740 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237208 none O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 48, 48, 194, 194, 194, 194, 194, 196, 196, 196, 196, 194, 1, 1, 6, 6, 6, 1, 1, 5, 5, 194, 194, 194, 196, 196, 194, 1, 1, 6] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 40, 41, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 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, 42]) total number of confs: 304 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237208 none O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 87, 87, 194, 194, 87, 87, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 194, 194, 201, 201, 201, 194, 194, 87, 87, 1, 1, 1, 5, 5, 1, 194, 194, 201] 201 rigid atoms, others: [34, 35, 36, 39, 12, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 40, 41, 42]) total number of confs: 796 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: REAL300000237208 none O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 11, 11, 89, 89, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 6, 6, 11, 11, 201, 201, 201, 201, 201, 201, 6, 6, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 377 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237208 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237208 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237208/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237208 Building REAL300000237209 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237209' /scratch/stefan/7769818/working/building/REAL300000237209 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237209 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237209/0 /scratch/stefan/7769818/working/building/REAL300000237209 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/209 `/scratch/stefan/7769818/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1) `REAL300000237209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237209 none O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 66, 66, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 201, 201, 201, 66, 66, 1, 1, 1, 3, 3, 1, 201, 201, 201] 201 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16, 21, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 33, 34, 35]) total number of confs: 340 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237209 none O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 110, 110, 38, 6, 38, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 201, 201, 201, 110, 109, 6, 6, 6, 1, 1, 6, 201, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 30, 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, 32, 33, 34, 35]) total number of confs: 410 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: REAL300000237209 none O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 11, 11, 69, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 11, 11, 201, 201, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 22, 23, 24, 33] 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]) total number of confs: 341 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237209 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237209 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237209/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237209 Building REAL300000237210 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237210' /scratch/stefan/7769818/working/building/REAL300000237210 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237210 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237210/0 /scratch/stefan/7769818/working/building/REAL300000237210 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/210 `/scratch/stefan/7769818/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1Cl) `REAL300000237210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237210 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 176, 70, 64, 70, 70, 22, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 201, 201, 70, 70, 22, 22, 1, 1, 1, 1, 1, 1, 70] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39]) total number of confs: 464 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237210 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 145, 79, 73, 79, 79, 36, 36, 17, 2, 17, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 79, 79, 79, 201, 201, 79, 79, 36, 35, 2, 2, 2, 1, 1, 2, 79] 201 rigid atoms, others: [36, 37, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 610 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: REAL300000237210 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 37, 7, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 26, 26, 1, 1, 5, 5, 70, 70, 70, 70, 70, 70, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 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]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237210 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237210 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237210/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237210 Building REAL300000237211 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237211' /scratch/stefan/7769818/working/building/REAL300000237211 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237211 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237211/0 /scratch/stefan/7769818/working/building/REAL300000237211 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/211 `/scratch/stefan/7769818/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC=C1C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1) `REAL300000237211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237211 none O=C([O-])C1=CC=CC=C1C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 122, 122, 188, 188, 122, 122, 40, 7, 40, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 7, 188, 188, 201, 201, 201, 201, 188, 188, 122, 122, 6, 7, 7, 1, 1, 7, 188, 188] 201 rigid atoms, others: [41, 42, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 691 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237211 none O=C([O-])C1=CC=CC=C1C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 3, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 42, 42, 165, 165, 165, 165, 165, 170, 170, 170, 170, 165, 1, 1, 4, 3, 4, 4, 1, 1, 5, 5, 165, 165, 165, 170, 170, 165, 1, 1] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 44, 45, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 270 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237211 none O=C([O-])C1=CC=CC=C1C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 82, 82, 165, 165, 82, 82, 12, 1, 12, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 165, 165, 201, 201, 201, 201, 165, 165, 82, 82, 1, 1, 1, 4, 4, 1, 165, 165] 201 rigid atoms, others: [38, 39, 40, 43, 15, 17, 18, 19, 20, 21, 22, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 44, 45]) total number of confs: 673 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: REAL300000237211 none O=C([O-])C1=CC=CC=C1C1=CC=C(C=CC(=O)C2=CC=CC(N3C=NN=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 13, 13, 84, 84, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 1, 4, 4, 13, 13, 201, 201, 201, 201, 201, 201, 4, 4] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 33, 30, 31] set([0, 2, 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: 376 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237211 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237211 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237211/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237211 Building REAL300000237212 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237212' /scratch/stefan/7769818/working/building/REAL300000237212 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237212 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237212/0 /scratch/stefan/7769818/working/building/REAL300000237212 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/212 `/scratch/stefan/7769818/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1) `REAL300000237212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237212 none COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 77, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 201, 201, 201, 201, 201, 201, 77, 77, 1, 1, 1, 3, 3, 1] 201 rigid atoms, others: [34, 35, 36, 39, 13, 15, 16, 17, 18, 19, 20, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 362 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237212 none COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 123, 45, 4, 45, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 201, 201, 201, 201, 201, 201, 123, 123, 4, 4, 4, 1, 1, 4] 201 rigid atoms, others: [37, 38, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 434 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: REAL300000237212 none COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC=CC(N2C=NN=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 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, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 71, 71, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 3, 3, 3, 1, 1, 1, 9, 9, 201, 201, 201, 201, 201, 201] 201 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]) total number of confs: 342 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237212 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237212 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237212/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237212 Building REAL300000237213 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237213' /scratch/stefan/7769818/working/building/REAL300000237213 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237213 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237213/0 /scratch/stefan/7769818/working/building/REAL300000237213 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/213 `/scratch/stefan/7769818/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C(F)=CC=C2S1) `REAL300000237213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237213 none O=C([O-])C1=CC2=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 15, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 77, 77, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 201, 201, 201, 201, 201, 201, 201, 77, 77, 1, 1, 1, 3, 3, 1, 201, 201] 201 rigid atoms, others: [32, 33, 36, 9, 11, 12, 13, 14, 15, 16, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 37, 38]) total number of confs: 345 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237213 none O=C([O-])C1=CC2=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 15, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 75, 75, 30, 6, 31, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 93, 93, 93, 93, 93, 93, 93, 75, 75, 6, 6, 6, 1, 1, 6, 93, 93] 93 rigid atoms, others: [34, 35, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) 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: REAL300000237213 none O=C([O-])C1=CC2=C(C=CC(=O)C3=CC=CC(N4C=NN=C4)=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 15, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 9, 64, 64, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 9, 9, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 22, 23, 24, 25, 26, 27, 28, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237213 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237213 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237213/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237213 Building REAL300000237214 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237214' /scratch/stefan/7769818/working/building/REAL300000237214 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237214 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237214/0 /scratch/stefan/7769818/working/building/REAL300000237214 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/214 `/scratch/stefan/7769818/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C=C1)C2=O) `REAL300000237214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237214 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 2, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1] 5 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237214 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 5 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 3, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237214 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237214 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237214/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237214 Building REAL300000237215 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237215' /scratch/stefan/7769818/working/building/REAL300000237215 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237215 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237215/0 /scratch/stefan/7769818/working/building/REAL300000237215 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/215 `/scratch/stefan/7769818/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(OCC(=O)[O-])C=C1)C2=O) `REAL300000237215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237215 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(OCC(=O)[O-])C=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [21, 21, 3, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 24, 34, 34, 1, 1, 3, 3, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 24, 24, 1, 1] 68 rigid atoms, others: [41, 42, 45, 14, 15, 16, 17, 18, 19, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 155 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237215 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(OCC(=O)[O-])C=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 9, 39, 42, 42, 3, 3, 1, 1, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 39, 39, 3, 3] 68 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 3, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 41, 42, 43, 44, 45, 46]) total number of confs: 165 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237215 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237215 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237215/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237215 Building REAL300000237216 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237216' /scratch/stefan/7769818/working/building/REAL300000237216 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237216 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237216/0 /scratch/stefan/7769818/working/building/REAL300000237216 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/216 `/scratch/stefan/7769818/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(OCCC(=O)[O-])C=C1)C2=O) `REAL300000237216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237216 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(OCCC(=O)[O-])C=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [11, 11, 3, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 10, 20, 23, 23, 1, 1, 3, 3, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 10, 10, 20, 20, 1, 1] 40 rigid atoms, others: [48, 49, 42, 43, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237216 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(OCCC(=O)[O-])C=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 9, 13, 24, 24, 24, 3, 3, 1, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 24, 24, 3, 3] 40 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 3, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237216 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237216 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237216/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237216 Building REAL300000237217 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237217' /scratch/stefan/7769818/working/building/REAL300000237217 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237217 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237217/0 /scratch/stefan/7769818/working/building/REAL300000237217 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/217 `/scratch/stefan/7769818/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(OC(C)C(=O)[O-])=C1)C2=O) `REAL300000237217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237217 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(OC(C)C(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 3, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 14, 14, 1, 3, 3, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 10, 10, 10, 10, 1] 21 rigid atoms, others: [49, 42, 43, 44, 14, 15, 16, 17, 18, 19, 20, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48]) total number of confs: 80 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237217 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(OC(C)C(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 7, 11, 11, 14, 14, 3, 1, 1, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 3] 21 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 3, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237217 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237217 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237217/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237217 Building REAL300000237218 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237218' /scratch/stefan/7769818/working/building/REAL300000237218 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237218 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237218/0 /scratch/stefan/7769818/working/building/REAL300000237218 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/218 `/scratch/stefan/7769818/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(OCCC(=O)[O-])=C1)C2=O) `REAL300000237218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237218 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(OCCC(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 2, 2, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 1] 6 rigid atoms, others: [49, 42, 43, 44, 14, 15, 16, 17, 18, 19, 20, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48]) total number of confs: 13 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237218 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(OCCC(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 2] 6 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 3, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 16 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237218 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237218 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237218/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237218 Building REAL300000237219 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237219' /scratch/stefan/7769818/working/building/REAL300000237219 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237219 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237219/0 /scratch/stefan/7769818/working/building/REAL300000237219 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/219 `/scratch/stefan/7769818/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(OCC(=O)[O-])=C1)C2=O) `REAL300000237219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237219 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(OCC(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 3, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 8, 9, 9, 1, 3, 3, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 8, 8, 1] 16 rigid atoms, others: [41, 42, 43, 14, 15, 16, 17, 18, 19, 20, 46, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45]) total number of confs: 52 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237219 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(OCC(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 5, 9, 10, 10, 3, 1, 1, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 3] 16 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 3, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 41, 42, 43, 44, 45, 46]) total number of confs: 50 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237219 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237219 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237219/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237219 Building REAL300000237220 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237220' /scratch/stefan/7769818/working/building/REAL300000237220 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237220 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237220/0 /scratch/stefan/7769818/working/building/REAL300000237220 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/220 `/scratch/stefan/7769818/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CN(CC(=O)[O-])N=N1)C2=O) `REAL300000237220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237220 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CN(CC(=O)[O-])N=N1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [36, 36, 6, 36, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 8, 13, 13, 1, 1, 6, 6, 36, 36, 36, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 8, 8] 48 rigid atoms, others: [39, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237220 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CN(CC(=O)[O-])N=N1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 21, 25, 25, 6, 6, 1, 1, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 21, 21] 48 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 3, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237220 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237220 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237220/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237220 Building REAL300000237221 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237221' /scratch/stefan/7769818/working/building/REAL300000237221 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237221 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237221/0 /scratch/stefan/7769818/working/building/REAL300000237221 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/221 `/scratch/stefan/7769818/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(C(=O)[O-])=C1)C2=O) `REAL300000237221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237221 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(C(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 5, 13, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 5, 5, 13, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 13 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237221 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(C(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 13 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 3, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28]) total number of confs: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237221 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237221 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237221/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237221 Building REAL300000237222 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237222' /scratch/stefan/7769818/working/building/REAL300000237222 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237222 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237222/0 /scratch/stefan/7769818/working/building/REAL300000237222 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/222 `/scratch/stefan/7769818/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=CS1)C2=O) `REAL300000237222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237222 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=CS1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.2', 'O.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, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 11, 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, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 9 rigid atoms, others: [38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237222 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=CS1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.2', 'O.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, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 11, 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, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 9 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 3, 38, 39, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237222 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237222 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237222/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237222 Building REAL300000237223 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237223' /scratch/stefan/7769818/working/building/REAL300000237223 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237223 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237223/0 /scratch/stefan/7769818/working/building/REAL300000237223 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/223 `/scratch/stefan/7769818/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C=C1Cl)C2=O) `REAL300000237223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237223 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C=C1Cl)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 4, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1] 7 rigid atoms, others: [40, 41, 42, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237223 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C=C1Cl)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 3, 4, 4, 4, 4, 4, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4] 7 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 3, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237223 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237223 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237223/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237223 Building REAL300000237224 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237224' /scratch/stefan/7769818/working/building/REAL300000237224 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237224 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237224/0 /scratch/stefan/7769818/working/building/REAL300000237224 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/224 `/scratch/stefan/7769818/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(C(=O)[O-])=C1Cl)C2=O) `REAL300000237224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237224 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(C(=O)[O-])=C1Cl)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 4, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 4, 4, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1] 10 rigid atoms, others: [40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237224 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(C(=O)[O-])=C1Cl)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 4, 4, 1, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4] 10 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 3, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237224 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237224 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237224/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237224 Building REAL300000237225 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237225' /scratch/stefan/7769818/working/building/REAL300000237225 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237225 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237225/0 /scratch/stefan/7769818/working/building/REAL300000237225 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/225 `/scratch/stefan/7769818/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(O)C(C(=O)[O-])=C1)C2=O) `REAL300000237225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237225 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(O)C(C(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [10, 10, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 5, 5, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 1] 20 rigid atoms, others: [40, 41, 43, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237225 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(O)C(C(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 5] 20 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 3, 40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237225 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237225 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237225/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237225 Building REAL300000237226 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237226' /scratch/stefan/7769818/working/building/REAL300000237226 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237226 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237226/0 /scratch/stefan/7769818/working/building/REAL300000237226 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/226 `/scratch/stefan/7769818/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=C(C)C=C1C)C2=O) `REAL300000237226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237226 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=C(C)C=C1C)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2, 1, 2, 2, 2] 10 rigid atoms, others: [41, 45, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 46, 47, 48]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237226 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=C(C)C=C1C)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 5, 5, 5, 5, 5, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5] 10 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 3, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237226 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237226 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237226/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237226 Building REAL300000237227 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237227' /scratch/stefan/7769818/working/building/REAL300000237227 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237227 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237227/0 /scratch/stefan/7769818/working/building/REAL300000237227 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/227 `/scratch/stefan/7769818/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(OC(C)C(=O)[O-])C=C1)C2=O) `REAL300000237227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237227 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(OC(C)C(=O)[O-])C=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [22, 22, 3, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 12, 27, 27, 38, 38, 1, 1, 3, 3, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 27, 27, 27, 27, 1, 1] 77 rigid atoms, others: [48, 49, 42, 43, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 180 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237227 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(OC(C)C(=O)[O-])C=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 13, 38, 38, 50, 50, 3, 3, 1, 1, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 38, 38, 38, 38, 3, 3] 77 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 3, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237227 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237227 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237227/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237227 Building REAL300000237228 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237228' /scratch/stefan/7769818/working/building/REAL300000237228 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237228 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237228/0 /scratch/stefan/7769818/working/building/REAL300000237228 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/228 `/scratch/stefan/7769818/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C(F)=C1)C2=O) `REAL300000237228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237228 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C(F)=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 5, 5, 12, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1] 12 rigid atoms, others: [40, 41, 42, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237228 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C(F)=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 5, 5, 1, 1, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5] 12 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 3, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237228 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237228 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237228/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237228 Building REAL300000237229 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237229' /scratch/stefan/7769818/working/building/REAL300000237229 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237229 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237229/0 /scratch/stefan/7769818/working/building/REAL300000237229 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/229 `/scratch/stefan/7769818/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C=CC(=O)[O-])O1)C2=O) `REAL300000237229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237229 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C=CC(=O)[O-])O1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 6, 37, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 11, 11, 22, 22, 1, 6, 6, 37, 37, 37, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 11, 11] 54 rigid atoms, others: [40, 41, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43]) total number of confs: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237229 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C=CC(=O)[O-])O1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 34, 34, 39, 39, 6, 1, 1, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 34, 34] 54 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 3, 40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237229 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237229 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237229/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237229 Building REAL300000237230 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237230' /scratch/stefan/7769818/working/building/REAL300000237230 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237230 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237230/0 /scratch/stefan/7769818/working/building/REAL300000237230 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/230 `/scratch/stefan/7769818/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(OC)C(C(=O)[O-])=C1)C2=O) `REAL300000237230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237230 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(OC)C(C(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 5, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 3, 1, 1, 3, 3, 1, 5, 5, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 3, 3, 3, 1] 33 rigid atoms, others: [41, 42, 46, 14, 15, 16, 17, 18, 19, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 54 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237230 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(OC)C(C(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 5, 5, 9, 9, 5, 1, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 5] 33 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 3, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 41, 42, 43, 44, 45, 46]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237230 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237230 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237230/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237230 Building REAL300000237231 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237231' /scratch/stefan/7769818/working/building/REAL300000237231 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237231 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237231/0 /scratch/stefan/7769818/working/building/REAL300000237231 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/231 `/scratch/stefan/7769818/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=CC=C1F)C2=O) `REAL300000237231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237231 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=CC=C1F)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 5, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1] 10 rigid atoms, others: [40, 41, 42, 14, 15, 16, 17, 18, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237231 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=CC=C1F)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5] 10 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 3, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29]) total number of confs: 14 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237231 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237231 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237231/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237231 Building REAL300000237232 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237232' /scratch/stefan/7769818/working/building/REAL300000237232 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237232 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237232/0 /scratch/stefan/7769818/working/building/REAL300000237232 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/232 `/scratch/stefan/7769818/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(F)C(C(=O)[O-])=C1)C2=O) `REAL300000237232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237232 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(F)C(C(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 5, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 5, 5, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1] 17 rigid atoms, others: [40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237232 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(F)C(C(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 9, 9, 5, 1, 1, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5] 17 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 3, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237232 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237232 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237232/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237232 Building REAL300000237233 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237233' /scratch/stefan/7769818/working/building/REAL300000237233 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237233 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237233/0 /scratch/stefan/7769818/working/building/REAL300000237233 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/233 `/scratch/stefan/7769818/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(CC(=O)[O-])C=C1)C2=O) `REAL300000237233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237233 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(CC(=O)[O-])C=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 3, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 3, 3, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 2, 2, 1, 1] 10 rigid atoms, others: [40, 41, 44, 45, 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, 39, 42, 43]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237233 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(CC(=O)[O-])C=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 4, 7, 7, 3, 3, 1, 1, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 3, 3] 10 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 3, 40, 41, 42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237233 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237233 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237233/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237233 Building REAL300000237234 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237234' /scratch/stefan/7769818/working/building/REAL300000237234 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237234 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237234/0 /scratch/stefan/7769818/working/building/REAL300000237234 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/234 `/scratch/stefan/7769818/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])S1)C2=O) `REAL300000237234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237234 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])S1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'O.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, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 11, 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, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 3, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1] 9 rigid atoms, others: [38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237234 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])S1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'O.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, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 11, 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, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 9 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 3, 38, 39, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27]) total number of confs: 12 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237234 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237234 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237234/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237234 Building REAL300000237235 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237235' /scratch/stefan/7769818/working/building/REAL300000237235 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237235 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237235/0 /scratch/stefan/7769818/working/building/REAL300000237235 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/235 `/scratch/stefan/7769818/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C=CC(=O)[O-])C=C1)C2=O) `REAL300000237235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237235 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C=CC(=O)[O-])C=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 3, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 3, 3, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 5, 5, 1, 1] 14 rigid atoms, others: [41, 42, 45, 14, 15, 16, 17, 18, 19, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 47 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237235 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C=CC(=O)[O-])C=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 8, 8, 10, 10, 3, 3, 1, 1, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 3, 3] 14 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 3, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 41, 42, 43, 44, 45, 46]) total number of confs: 49 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237235 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237235 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237235/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237235 Building REAL300000237236 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237236' /scratch/stefan/7769818/working/building/REAL300000237236 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237236 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237236/0 /scratch/stefan/7769818/working/building/REAL300000237236 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/236 `/scratch/stefan/7769818/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(F)=C(C(=O)[O-])C=C1F)C2=O) `REAL300000237236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237236 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(F)=C(C(=O)[O-])C=C1F)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.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, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 11, 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, 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 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 5, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 5, 5, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 14 rigid atoms, others: [41, 42, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237236 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(F)=C(C(=O)[O-])C=C1F)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.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, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 11, 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, 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 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 4, 4, 8, 8, 5, 5, 5, 1, 1, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 14 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 3, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237236 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237236 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237236/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237236 Building REAL300000237237 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237237' /scratch/stefan/7769818/working/building/REAL300000237237 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237237 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237237/0 /scratch/stefan/7769818/working/building/REAL300000237237 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/237 `/scratch/stefan/7769818/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=C3C(=CC=C1)NN=C3C(=O)[O-])C2=O) `REAL300000237237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237237 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=C3C(=CC=C1)NN=C3C(=O)[O-])C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 4, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1] 11 rigid atoms, others: [42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237237 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=C3C(=CC=C1)NN=C3C(=O)[O-])C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 11 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 3, 42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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 /scratch/stefan/7769818/working/building/REAL300000237237 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237237 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237237/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237237 Building REAL300000237238 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237238' /scratch/stefan/7769818/working/building/REAL300000237238 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237238 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237238/0 /scratch/stefan/7769818/working/building/REAL300000237238 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/238 `/scratch/stefan/7769818/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CNC3=CC=C(C(=O)[O-])C=C13)C2=O) `REAL300000237238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237238 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CNC3=CC=C(C(=O)[O-])C=C13)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1] 9 rigid atoms, others: [42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237238 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CNC3=CC=C(C(=O)[O-])C=C13)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 9 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 3, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 42, 43, 44, 45, 46]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237238 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237238 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237238/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237238 Building REAL300000237239 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237239' /scratch/stefan/7769818/working/building/REAL300000237239 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237239 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237239/0 /scratch/stefan/7769818/working/building/REAL300000237239 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/239 `/scratch/stefan/7769818/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])N=C1)C2=O) `REAL300000237239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237239 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])N=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 3, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1] 9 rigid atoms, others: [39, 40, 41, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237239 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])N=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3] 9 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 3, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28]) total number of confs: 18 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237239 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237239 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237239/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237239 Building REAL300000237240 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237240' /scratch/stefan/7769818/working/building/REAL300000237240 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237240 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237240/0 /scratch/stefan/7769818/working/building/REAL300000237240 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/240 `/scratch/stefan/7769818/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C(O)=C1)C2=O) `REAL300000237240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237240 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C(O)=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 5, 5, 12, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 1] 24 rigid atoms, others: [40, 41, 43, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237240 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C(O)=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 5, 5, 1, 1, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 5] 24 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 3, 40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237240 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237240 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237240/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237240 Building REAL300000237241 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237241' /scratch/stefan/7769818/working/building/REAL300000237241 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237241 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237241/0 /scratch/stefan/7769818/working/building/REAL300000237241 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/241 `/scratch/stefan/7769818/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C)C(C(=O)[O-])=C1)C2=O) `REAL300000237241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237241 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C)C(C(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 5, 5, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 2, 1] 8 rigid atoms, others: [40, 41, 45, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 33 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237241 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C)C(C(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 8 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 3, 40, 41, 42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29]) total number of confs: 14 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237241 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237241 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237241/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237241 Building REAL300000237242 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237242' /scratch/stefan/7769818/working/building/REAL300000237242 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237242 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237242/0 /scratch/stefan/7769818/working/building/REAL300000237242 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/242 `/scratch/stefan/7769818/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=C(Cl)S1)C2=O) `REAL300000237242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237242 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=C(Cl)S1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.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, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 11, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 5, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 5, 5, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1] 17 rigid atoms, others: [39, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237242 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=C(Cl)S1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.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, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 11, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 5, 5, 5, 1, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5] 17 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 3, 39, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237242 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237242 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237242/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237242 Building REAL300000237243 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237243' /scratch/stefan/7769818/working/building/REAL300000237243 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237243 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237243/0 /scratch/stefan/7769818/working/building/REAL300000237243 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/243 `/scratch/stefan/7769818/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=C(C)O1)C2=O) `REAL300000237243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237243 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=C(C)O1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 5, 5, 12, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2] 12 rigid atoms, others: [39, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237243 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=C(C)O1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 5, 5, 5, 1, 1, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 12 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 3, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237243 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237243 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237243/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237243 Building REAL300000237244 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237244' /scratch/stefan/7769818/working/building/REAL300000237244 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237244 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237244/0 /scratch/stefan/7769818/working/building/REAL300000237244 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/244 `/scratch/stefan/7769818/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=NN1C)C2=O) `REAL300000237244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237244 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=NN1C)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2] 9 rigid atoms, others: [39, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237244 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=NN1C)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 9 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 3, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28]) total number of confs: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237244 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237244 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237244/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237244 Building REAL300000237245 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237245' /scratch/stefan/7769818/working/building/REAL300000237245 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237245 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237245/0 /scratch/stefan/7769818/working/building/REAL300000237245 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/245 `/scratch/stefan/7769818/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CN=CC(C(=O)[O-])=C1)C2=O) `REAL300000237245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237245 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CN=CC(C(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 5, 13, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1] 13 rigid atoms, others: [39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237245 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CN=CC(C(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5] 13 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 3, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28]) total number of confs: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237245 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237245 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237245/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237245 Building REAL300000237246 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237246' /scratch/stefan/7769818/working/building/REAL300000237246 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237246 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237246/0 /scratch/stefan/7769818/working/building/REAL300000237246 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/246 `/scratch/stefan/7769818/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=CO1)C2=O) `REAL300000237246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237246 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=CO1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.2', 'O.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, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 11, 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, 7, 7, 7, 7, 2, 2, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 3, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1] 9 rigid atoms, others: [38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237246 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=CO1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.2', 'O.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, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 11, 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, 7, 7, 7, 7, 2, 2, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 9 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 3, 38, 39, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27]) total number of confs: 12 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237246 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237246 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237246/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237246 Building REAL300000237247 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237247' /scratch/stefan/7769818/working/building/REAL300000237247 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237247 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237247/0 /scratch/stefan/7769818/working/building/REAL300000237247 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/247 `/scratch/stefan/7769818/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=CC=C1OC)C2=O) `REAL300000237247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237247 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=CC=C1OC)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 5, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 4, 5, 5, 17, 17, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 4, 4, 4] 17 rigid atoms, others: [41, 42, 43, 14, 15, 16, 17, 18, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237247 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(C(=O)[O-])=CC=C1OC)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 1, 1, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9] 17 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 3, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 41, 42, 43, 44, 45, 46]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237247 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237247 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237247/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237247 Building REAL300000237248 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237248' /scratch/stefan/7769818/working/building/REAL300000237248 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237248 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237248/0 /scratch/stefan/7769818/working/building/REAL300000237248 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/248 `/scratch/stefan/7769818/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C=C1[N+](=O)[O-])C2=O) `REAL300000237248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237248 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C=C1[N+](=O)[O-])C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1] 9 rigid atoms, others: [42, 43, 44, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237248 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C=C1[N+](=O)[O-])C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5] 9 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 3, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 14 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237248 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237248 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237248/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237248 Building REAL300000237249 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237249' /scratch/stefan/7769818/working/building/REAL300000237249 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237249 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237249/0 /scratch/stefan/7769818/working/building/REAL300000237249 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/249 `/scratch/stefan/7769818/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(CC(=O)[O-])=C1)C2=O) `REAL300000237249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237249 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(CC(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 5, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 5, 5, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 2, 1] 16 rigid atoms, others: [40, 41, 42, 45, 14, 15, 16, 17, 18, 19, 20, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237249 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(CC(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 8, 9, 9, 5, 1, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 2, 8, 8, 5] 16 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 3, 40, 41, 42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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 /scratch/stefan/7769818/working/building/REAL300000237249 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237249 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237249/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237249 Building REAL300000237250 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237250' /scratch/stefan/7769818/working/building/REAL300000237250 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237250 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237250/0 /scratch/stefan/7769818/working/building/REAL300000237250 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/250 `/scratch/stefan/7769818/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C(OC)=C1)C2=O) `REAL300000237250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237250 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C(OC)=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 7, 28, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 1, 7, 7, 28, 28, 28, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 3, 3, 3, 1] 34 rigid atoms, others: [41, 42, 14, 15, 16, 17, 18, 19, 46, 22, 23, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237250 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C(OC)=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 7, 7, 10, 7, 1, 1, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 7] 34 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 3, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 41, 42, 43, 44, 45, 46]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237250 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237250 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237250/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237250 Building REAL300000237251 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237251' /scratch/stefan/7769818/working/building/REAL300000237251 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237251 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237251/0 /scratch/stefan/7769818/working/building/REAL300000237251 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/251 `/scratch/stefan/7769818/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=C(F)C=C(C(=O)[O-])C=C1F)C2=O) `REAL300000237251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237251 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=C(F)C=C(C(=O)[O-])C=C1F)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.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, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 11, 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, 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 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 3, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1] 5 rigid atoms, others: [41, 42, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237251 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=C(F)C=C(C(=O)[O-])C=C1F)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.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, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 11, 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, 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 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 3, 3, 3, 3, 3, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 5 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 3, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237251 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237251 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237251/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237251 Building REAL300000237252 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237252' /scratch/stefan/7769818/working/building/REAL300000237252 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237252 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237252/0 /scratch/stefan/7769818/working/building/REAL300000237252 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/252 `/scratch/stefan/7769818/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CSC(C(=O)[O-])=C1)C2=O) `REAL300000237252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237252 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CSC(C(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.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, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 1, 11, 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, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 4, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 4, 4, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1] 9 rigid atoms, others: [38, 39, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237252 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CSC(C(=O)[O-])=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.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, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 1, 11, 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, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 9 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 3, 38, 39, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237252 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237252 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237252/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237252 Building REAL300000237253 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237253' /scratch/stefan/7769818/working/building/REAL300000237253 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237253 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237253/0 /scratch/stefan/7769818/working/building/REAL300000237253 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/253 `/scratch/stefan/7769818/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(F)=C(C(=O)[O-])C(F)=C1)C2=O) `REAL300000237253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237253 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(F)=C(C(=O)[O-])C(F)=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.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, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 1, 11, 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, 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 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 3, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 3, 3, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1] 7 rigid atoms, others: [41, 42, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237253 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC(F)=C(C(=O)[O-])C(F)=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.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, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 1, 11, 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, 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 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 4, 4, 3, 3, 3, 1, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 7 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 3, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237253 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237253 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237253/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237253 Building REAL300000237254 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237254' /scratch/stefan/7769818/working/building/REAL300000237254 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237254 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237254/0 /scratch/stefan/7769818/working/building/REAL300000237254 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/254 `/scratch/stefan/7769818/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC3=C(C=C(C(=O)[O-])N3)O1)C2=O) `REAL300000237254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237254 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC3=C(C=C(C(=O)[O-])N3)O1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 5, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1] 9 rigid atoms, others: [41, 42, 43, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237254 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC3=C(C=C(C(=O)[O-])N3)O1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5] 9 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 3, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237254 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237254 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237254/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237254 Building REAL300000237255 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237255' /scratch/stefan/7769818/working/building/REAL300000237255 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237255 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237255/0 /scratch/stefan/7769818/working/building/REAL300000237255 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/255 `/scratch/stefan/7769818/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C3OC(C(=O)[O-])=CC3=C1)C2=O) `REAL300000237255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237255 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C3OC(C(=O)[O-])=CC3=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 9 rigid atoms, others: [42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237255 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C3OC(C(=O)[O-])=CC3=C1)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 9 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 3, 42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237255 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237255 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237255/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237255 Building REAL300000237256 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237256' /scratch/stefan/7769818/working/building/REAL300000237256 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237256 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237256/0 /scratch/stefan/7769818/working/building/REAL300000237256 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/256 `/scratch/stefan/7769818/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CN3C(C(=O)[O-])=CN=C13)C2=O) `REAL300000237256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237256 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CN3C(C(=O)[O-])=CN=C13)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 9 rigid atoms, others: [42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237256 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CN3C(C(=O)[O-])=CN=C13)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 9 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 3, 42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237256 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237256 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237256/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237256 Building REAL300000237257 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237257' /scratch/stefan/7769818/working/building/REAL300000237257 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237257 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237257/0 /scratch/stefan/7769818/working/building/REAL300000237257 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/257 `/scratch/stefan/7769818/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CN=C3C=CC(C(=O)[O-])=CN13)C2=O) `REAL300000237257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237257 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CN=C3C=CC(C(=O)[O-])=CN13)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 5, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 9 rigid atoms, others: [42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237257 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CN=C3C=CC(C(=O)[O-])=CN13)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 9 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 3, 42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237257 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237257 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237257/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237257 Building REAL300000237258 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237258' /scratch/stefan/7769818/working/building/REAL300000237258 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237258 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237258/0 /scratch/stefan/7769818/working/building/REAL300000237258 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/258 `/scratch/stefan/7769818/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(C(=O)[O-])=C1F)C2=O) `REAL300000237258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237258 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(C(=O)[O-])=C1F)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 5, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 5, 5, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1] 18 rigid atoms, others: [40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237258 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=CC(C(=O)[O-])=C1F)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 5, 5, 1, 1, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5] 18 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 3, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237258 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237258 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237258/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237258 Building REAL300000237259 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237259' /scratch/stefan/7769818/working/building/REAL300000237259 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237259 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237259/0 /scratch/stefan/7769818/working/building/REAL300000237259 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/259 `/scratch/stefan/7769818/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C=C1OC)C2=O) `REAL300000237259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237259 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C=C1OC)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 4, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 4, 4, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 2, 2] 9 rigid atoms, others: [41, 42, 43, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237259 none COC(=O)C1=CC=C2C(=C1)CCCC(=CC1=CC=C(C(=O)[O-])C=C1OC)C2=O 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.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', '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, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 1, 1, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5] 9 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 3, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 41, 42, 43, 44, 45, 46]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237259 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237259 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237259/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237259 Building REAL300000237260 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237260' /scratch/stefan/7769818/working/building/REAL300000237260 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237260 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237260/0 /scratch/stefan/7769818/working/building/REAL300000237260 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/260 `/scratch/stefan/7769818/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1) `REAL300000237260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237260 none O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2] 2 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 26, 27]) total number of confs: 3 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237260 none O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1] 2 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25]) total number of confs: 5 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237260 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237260 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237260/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237260 Building REAL300000237261 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237261' /scratch/stefan/7769818/working/building/REAL300000237261 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237261 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237261/0 /scratch/stefan/7769818/working/building/REAL300000237261 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/261 `/scratch/stefan/7769818/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1) `REAL300000237261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237261 none O=C([O-])CCOC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 41, 34, 11, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 43, 43, 34, 34, 7, 7, 1, 1, 1, 1, 7, 7] 43 rigid atoms, others: [32, 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, 34, 33, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 167 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237261 none O=C([O-])CCOC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [24, 16, 22, 11, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 16, 16, 11, 11, 1, 1, 7, 7, 7, 7, 1, 1] 43 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32]) total number of confs: 100 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237261 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237261 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237261/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237261 Building REAL300000237262 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237262' /scratch/stefan/7769818/working/building/REAL300000237262 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237262 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237262/0 /scratch/stefan/7769818/working/building/REAL300000237262 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/262 `/scratch/stefan/7769818/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1) `REAL300000237262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237262 none O=C([O-])CCOC1=CC=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 100, 75, 29, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 101, 101, 75, 75, 7, 7, 7, 1, 1, 1, 1, 7] 101 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 364 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237262 none O=C([O-])CCOC1=CC=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [46, 34, 43, 24, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 34, 34, 24, 24, 1, 1, 1, 7, 7, 7, 7, 1] 101 rigid atoms, others: [34, 5, 6, 7, 8, 9, 10, 11, 22, 27, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 186 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237262 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237262 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237262/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237262 Building REAL300000237263 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237263' /scratch/stefan/7769818/working/building/REAL300000237263 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237263 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237263/0 /scratch/stefan/7769818/working/building/REAL300000237263 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/263 `/scratch/stefan/7769818/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=C2CC3=C(C=C(Br)S3)C2=O)N=N1) `REAL300000237263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237263 none O=C([O-])CN1C=C(C=C2CC3=C(C=C(Br)S3)C2=O)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 22, 22, 9, 1, 1, 1, 1] 22 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237263 none O=C([O-])CN1C=C(C=C2CC3=C(C=C(Br)S3)C2=O)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 6, 6, 1, 9, 9, 9, 9] 22 rigid atoms, others: [3, 4, 5, 6, 7, 18, 19, 22] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 23, 24, 25, 26]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237263 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237263 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237263/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237263 Building REAL300000237264 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237264' /scratch/stefan/7769818/working/building/REAL300000237264 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237264 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237264/0 /scratch/stefan/7769818/working/building/REAL300000237264 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/264 `/scratch/stefan/7769818/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1) `REAL300000237264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237264 none O=C([O-])C1=CC=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 1, 1, 4] 4 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 27]) total number of confs: 5 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237264 none O=C([O-])C1=CC=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 1] 4 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 9 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237264 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237264 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237264/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237264 Building REAL300000237265 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237265' /scratch/stefan/7769818/working/building/REAL300000237265 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237265 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237265/0 /scratch/stefan/7769818/working/building/REAL300000237265 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/265 `/scratch/stefan/7769818/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1) `REAL300000237265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237265 none O=C([O-])C1=CSC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 3] 3 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 18, 19, 24]) total number of confs: 4 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237265 none O=C([O-])C1=CSC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3, 3, 3, 1] 3 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237265 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237265 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237265/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237265 Building REAL300000237266 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237266' /scratch/stefan/7769818/working/building/REAL300000237266 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237266 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237266/0 /scratch/stefan/7769818/working/building/REAL300000237266 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/266 `/scratch/stefan/7769818/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C(Cl)=C1) `REAL300000237266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237266 none O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3] 3 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 27]) total number of confs: 9 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237266 none O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1] 3 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237266 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237266 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237266/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237266 Building REAL300000237267 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237267' /scratch/stefan/7769818/working/building/REAL300000237267 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237267 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237267/0 /scratch/stefan/7769818/working/building/REAL300000237267 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/267 `/scratch/stefan/7769818/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)C(C=C2CC3=C(C=C(Br)S3)C2=O)=CC=C1) `REAL300000237267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237267 none O=C([O-])C1=C(Cl)C(C=C2CC3=C(C=C(Br)S3)C2=O)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5] 5 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 25, 26, 27]) total number of confs: 6 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237267 none O=C([O-])C1=C(Cl)C(C=C2CC3=C(C=C(Br)S3)C2=O)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1] 5 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237267 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237267 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237267/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237267 Building REAL300000237268 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237268' /scratch/stefan/7769818/working/building/REAL300000237268 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237268 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237268/0 /scratch/stefan/7769818/working/building/REAL300000237268 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/268 `/scratch/stefan/7769818/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=CC=C1O) `REAL300000237268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237268 none O=C([O-])C1=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 14] 14 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 26, 27, 28]) total number of confs: 22 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237268 none O=C([O-])C1=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 1, 3, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 2] 14 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 28]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237268 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237268 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237268/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237268 Building REAL300000237269 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237269' /scratch/stefan/7769818/working/building/REAL300000237269 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237269 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237269/0 /scratch/stefan/7769818/working/building/REAL300000237269 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/269 `/scratch/stefan/7769818/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=C1CC2=C(C=C(Br)S2)C1=O) `REAL300000237269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237269 none CC1=CC(C)=C(C(=O)[O-])C=C1C=C1CC2=C(C=C(Br)S2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1] 4 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 5 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237269 none CC1=CC(C)=C(C(=O)[O-])C=C1C=C1CC2=C(C=C(Br)S2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 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, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 2, 2, 2, 1, 4, 4, 4, 4] 4 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 25, 29] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237269 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237269 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237269/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237269 Building REAL300000237270 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237270' /scratch/stefan/7769818/working/building/REAL300000237270 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237270 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237270/0 /scratch/stefan/7769818/working/building/REAL300000237270 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/270 `/scratch/stefan/7769818/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1)C(=O)[O-]) `REAL300000237270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237270 none CC(OC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [33, 13, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 33, 35, 35, 34, 34, 33, 33, 7, 7, 1, 1, 1, 1, 7, 7] 35 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 33, 34, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 134 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237270 none CC(OC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [21, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 21, 28, 28, 21, 21, 21, 21, 1, 1, 7, 7, 7, 7, 1, 1] 35 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 18, 19, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32]) total number of confs: 107 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237270 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237270 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237270/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237270 Building REAL300000237271 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237271' /scratch/stefan/7769818/working/building/REAL300000237271 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237271 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237271/0 /scratch/stefan/7769818/working/building/REAL300000237271 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/271 `/scratch/stefan/7769818/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1F) `REAL300000237271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237271 none O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3] 3 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 27]) total number of confs: 4 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237271 none O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1] 3 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237271 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237271 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237271/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237271 Building REAL300000237272 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237272' /scratch/stefan/7769818/working/building/REAL300000237272 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237272 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237272/0 /scratch/stefan/7769818/working/building/REAL300000237272 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/272 `/scratch/stefan/7769818/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)O1) `REAL300000237272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237272 none O=C([O-])C=CC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 22, 22, 8, 8, 1, 1, 1, 1] 22 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237272 none O=C([O-])C=CC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 13, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 7, 6, 1, 1, 8, 8, 8, 8] 22 rigid atoms, others: [4, 5, 6, 7, 8, 9, 20, 23, 24] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 25, 26, 27, 28]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237272 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237272 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237272/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237272 Building REAL300000237273 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237273' /scratch/stefan/7769818/working/building/REAL300000237273 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237273 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237273/0 /scratch/stefan/7769818/working/building/REAL300000237273 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/273 `/scratch/stefan/7769818/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1C(=O)[O-]) `REAL300000237273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237273 none COC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 14, 14, 14, 7, 7, 1, 1, 1, 1, 7] 14 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237273 none COC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 7, 7, 7, 7, 1] 14 rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 18, 19, 25, 26, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237273 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237273 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237273/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237273 Building REAL300000237274 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237274' /scratch/stefan/7769818/working/building/REAL300000237274 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237274 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237274/0 /scratch/stefan/7769818/working/building/REAL300000237274 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/274 `/scratch/stefan/7769818/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(F)C(C=C2CC3=C(C=C(Br)S3)C2=O)=C1) `REAL300000237274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237274 none O=C([O-])C1=CC=C(F)C(C=C2CC3=C(C=C(Br)S3)C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 5] 5 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 27]) total number of confs: 6 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237274 none O=C([O-])C1=CC=C(F)C(C=C2CC3=C(C=C(Br)S3)C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5, 5, 5, 1] 5 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 27] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237274 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237274 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237274/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237274 Building REAL300000237275 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237275' /scratch/stefan/7769818/working/building/REAL300000237275 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237275 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237275/0 /scratch/stefan/7769818/working/building/REAL300000237275 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/275 `/scratch/stefan/7769818/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=CC=C1F) `REAL300000237275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237275 none O=C([O-])C1=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7] 7 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 26, 27]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237275 none O=C([O-])C1=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237275 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237275 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237275/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237275 Building REAL300000237276 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237276' /scratch/stefan/7769818/working/building/REAL300000237276 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237276 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237276/0 /scratch/stefan/7769818/working/building/REAL300000237276 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/276 `/scratch/stefan/7769818/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1) `REAL300000237276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237276 none O=C([O-])CC1=CC=C(C=C2CC3=C(C=C(Br)S3)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', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.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, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 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, 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 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, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 29, 30]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237276 none O=C([O-])CC1=CC=C(C=C2CC3=C(C=C(Br)S3)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', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.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, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 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, 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 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, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 2, 2, 1, 1, 3, 3, 3, 3, 1, 1] 3 rigid atoms, others: [3, 4, 5, 6, 7, 8, 19, 20, 23, 24, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237276 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237276 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237276/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237276 Building REAL300000237277 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237277' /scratch/stefan/7769818/working/building/REAL300000237277 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237277 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237277/0 /scratch/stefan/7769818/working/building/REAL300000237277 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/277 `/scratch/stefan/7769818/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)S1) `REAL300000237277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237277 none O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 14, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1] 4 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 18, 19, 20]) total number of confs: 5 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237277 none O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 14, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 4 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237277 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237277 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237277/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237277 Building REAL300000237278 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237278' /scratch/stefan/7769818/working/building/REAL300000237278 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237278 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237278/0 /scratch/stefan/7769818/working/building/REAL300000237278 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/278 `/scratch/stefan/7769818/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1) `REAL300000237278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237278 none O=C([O-])C=CC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7] 7 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 30 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237278 none O=C([O-])C=CC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 3, 3, 1, 1, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [4, 5, 6, 7, 8, 9, 20, 21, 24, 25, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29]) total number of confs: 29 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237278 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237278 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237278/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237278 Building REAL300000237279 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237279' /scratch/stefan/7769818/working/building/REAL300000237279 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237279 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237279/0 /scratch/stefan/7769818/working/building/REAL300000237279 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/279 `/scratch/stefan/7769818/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1F) `REAL300000237279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237279 none O=C([O-])C1=CC(F)=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1, 1, 7] 7 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 27]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237279 none O=C([O-])C1=CC(F)=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7, 1] 7 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237279 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237279 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237279/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237279 Building REAL300000237280 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237280' /scratch/stefan/7769818/working/building/REAL300000237280 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237280 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237280/0 /scratch/stefan/7769818/working/building/REAL300000237280 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/280 `/scratch/stefan/7769818/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NNC2=CC=CC(C=C3CC4=C(C=C(Br)S4)C3=O)=C21) `REAL300000237280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237280 none O=C([O-])C1=NNC2=CC=CC(C=C3CC4=C(C=C(Br)S4)C3=O)=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 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] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 1, 1] 6 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26]) total number of confs: 7 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237280 none O=C([O-])C1=NNC2=CC=CC(C=C3CC4=C(C=C(Br)S4)C3=O)=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 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] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6] 6 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237280 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237280 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237280/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237280 Building REAL300000237281 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237281' /scratch/stefan/7769818/working/building/REAL300000237281 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237281 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237281/0 /scratch/stefan/7769818/working/building/REAL300000237281 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/281 `/scratch/stefan/7769818/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2NC=C(C=C3CC4=C(C=C(Br)S4)C3=O)C2=C1) `REAL300000237281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237281 none O=C([O-])C1=CC=C2NC=C(C=C3CC4=C(C=C(Br)S4)C3=O)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7] 7 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237281 none O=C([O-])C1=CC=C2NC=C(C=C3CC4=C(C=C(Br)S4)C3=O)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237281 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237281 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237281/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237281 Building REAL300000237282 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237282' /scratch/stefan/7769818/working/building/REAL300000237282 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237282 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237282/0 /scratch/stefan/7769818/working/building/REAL300000237282 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/282 `/scratch/stefan/7769818/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=N1) `REAL300000237282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237282 none O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 1, 1, 3] 3 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 26]) total number of confs: 4 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237282 none O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25]) total number of confs: 7 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237282 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237282 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237282/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237282 Building REAL300000237283 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237283' /scratch/stefan/7769818/working/building/REAL300000237283 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237283 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237283/0 /scratch/stefan/7769818/working/building/REAL300000237283 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/283 `/scratch/stefan/7769818/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1O) `REAL300000237283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237283 none O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 6] 6 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 27, 28]) total number of confs: 10 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237283 none O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 2] 6 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 28]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237283 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237283 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237283/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237283 Building REAL300000237284 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237284' /scratch/stefan/7769818/working/building/REAL300000237284 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237284 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237284/0 /scratch/stefan/7769818/working/building/REAL300000237284 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/284 `/scratch/stefan/7769818/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1C(=O)[O-]) `REAL300000237284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237284 none CC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7] 7 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29] set([0, 1, 2, 3, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237284 none CC1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 7, 7, 7, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 24, 25, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 26, 27, 28, 29]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237284 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237284 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237284/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237284 Building REAL300000237285 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237285' /scratch/stefan/7769818/working/building/REAL300000237285 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237285 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237285/0 /scratch/stefan/7769818/working/building/REAL300000237285 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/285 `/scratch/stefan/7769818/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)SC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1) `REAL300000237285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237285 none O=C([O-])C1=C(Cl)SC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 1, 1, 1, 1, 7] 7 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 19, 24]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237285 none O=C([O-])C1=C(Cl)SC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 1] 7 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 24] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237285 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237285 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237285/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237285 Building REAL300000237286 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237286' /scratch/stefan/7769818/working/building/REAL300000237286 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237286 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237286/0 /scratch/stefan/7769818/working/building/REAL300000237286 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/286 `/scratch/stefan/7769818/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=C2CC3=C(C=C(Br)S3)C2=O)O1) `REAL300000237286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237286 none CC1=C(C(=O)[O-])C=C(C=C2CC3=C(C=C(Br)S3)C2=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 1, 1] 9 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23]) total number of confs: 10 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237286 none CC1=C(C(=O)[O-])C=C(C=C2CC3=C(C=C(Br)S3)C2=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 1, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 19, 23] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237286 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237286 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237286/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237286 Building REAL300000237287 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237287' /scratch/stefan/7769818/working/building/REAL300000237287 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237287 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237287/0 /scratch/stefan/7769818/working/building/REAL300000237287 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/287 `/scratch/stefan/7769818/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=C1CC2=C(C=C(Br)S2)C1=O) `REAL300000237287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237287 none CN1N=C(C(=O)[O-])C=C1C=C1CC2=C(C=C(Br)S2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 1, 1] 3 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23]) total number of confs: 4 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237287 none CN1N=C(C(=O)[O-])C=C1C=C1CC2=C(C=C(Br)S2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237287 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237287 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237287/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237287 Building REAL300000237288 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237288' /scratch/stefan/7769818/working/building/REAL300000237288 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237288 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237288/0 /scratch/stefan/7769818/working/building/REAL300000237288 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/288 `/scratch/stefan/7769818/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1) `REAL300000237288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237288 none O=C([O-])C1=CN=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 4] 4 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 26]) total number of confs: 5 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237288 none O=C([O-])C1=CN=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4, 1] 4 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237288 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237288 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237288/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237288 Building REAL300000237289 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237289' /scratch/stefan/7769818/working/building/REAL300000237289 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237289 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237289/0 /scratch/stefan/7769818/working/building/REAL300000237289 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/289 `/scratch/stefan/7769818/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=COC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1) `REAL300000237289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237289 none O=C([O-])C1=COC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 5] 5 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 18, 19, 24]) total number of confs: 6 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237289 none O=C([O-])C1=COC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 1] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237289 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237289 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237289/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237289 Building REAL300000237290 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237290' /scratch/stefan/7769818/working/building/REAL300000237290 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237290 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237290/0 /scratch/stefan/7769818/working/building/REAL300000237290 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/290 `/scratch/stefan/7769818/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=C1CC2=C(C=C(Br)S2)C1=O) `REAL300000237290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237290 none COC1=CC=C(C(=O)[O-])C=C1C=C1CC2=C(C=C(Br)S2)C1=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', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', '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, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 7 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237290 none COC1=CC=C(C(=O)[O-])C=C1C=C1CC2=C(C=C(Br)S2)C1=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', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', '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, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237290 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237290 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237290/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237290 Building REAL300000237291 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237291' /scratch/stefan/7769818/working/building/REAL300000237291 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237291 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237291/0 /scratch/stefan/7769818/working/building/REAL300000237291 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/291 `/scratch/stefan/7769818/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C([N+](=O)[O-])=C1) `REAL300000237291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237291 none O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3] 3 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 24, 29]) total number of confs: 9 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237291 none O=C([O-])C1=CC=C(C=C2CC3=C(C=C(Br)S3)C2=O)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 22, 23, 24, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 25, 26, 27, 28]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237291 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237291 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237291/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237291 Building REAL300000237292 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237292' /scratch/stefan/7769818/working/building/REAL300000237292 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237292 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237292/0 /scratch/stefan/7769818/working/building/REAL300000237292 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/292 `/scratch/stefan/7769818/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1) `REAL300000237292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237292 none O=C([O-])CC1=CC=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 7, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 1, 7, 7, 1, 1, 1, 1, 7] 12 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 30]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237292 none O=C([O-])CC1=CC=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 2, 2, 1, 1, 1, 7, 7, 7, 7, 1] 12 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 20, 23, 24, 25, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 26, 27, 28, 29]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237292 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237292 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237292/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237292 Building REAL300000237293 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237293' /scratch/stefan/7769818/working/building/REAL300000237293 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237293 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237293/0 /scratch/stefan/7769818/working/building/REAL300000237293 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/293 `/scratch/stefan/7769818/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=CC=C1C(=O)[O-]) `REAL300000237293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237293 none COC1=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 1, 1, 1, 1, 7, 7] 9 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29] set([0, 1, 2, 3, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 20 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237293 none COC1=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 7, 7, 7, 7, 1, 1] 9 rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 18, 19, 25, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237293 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237293 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237293/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237293 Building REAL300000237294 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237294' /scratch/stefan/7769818/working/building/REAL300000237294 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237294 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237294/0 /scratch/stefan/7769818/working/building/REAL300000237294 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/294 `/scratch/stefan/7769818/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=C2CC3=C(C=C(Br)S3)C2=O)C(F)=C1) `REAL300000237294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237294 none O=C([O-])C1=CC(F)=C(C=C2CC3=C(C=C(Br)S3)C2=O)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 2] 2 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 27]) total number of confs: 10 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237294 none O=C([O-])C1=CC(F)=C(C=C2CC3=C(C=C(Br)S3)C2=O)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 1] 2 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 9 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237294 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237294 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237294/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237294 Building REAL300000237295 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237295' /scratch/stefan/7769818/working/building/REAL300000237295 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237295 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237295/0 /scratch/stefan/7769818/working/building/REAL300000237295 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/295 `/scratch/stefan/7769818/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=CS1) `REAL300000237295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237295 none O=C([O-])C1=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 14, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 4] 4 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 17, 18, 19, 24]) total number of confs: 5 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237295 none O=C([O-])C1=CC(C=C2CC3=C(C=C(Br)S3)C2=O)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 14, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4, 1] 4 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237295 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237295 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237295/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237295 Building REAL300000237296 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237296' /scratch/stefan/7769818/working/building/REAL300000237296 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237296 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237296/0 /scratch/stefan/7769818/working/building/REAL300000237296 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/296 `/scratch/stefan/7769818/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1F) `REAL300000237296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237296 none O=C([O-])C1=C(F)C=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 1, 1, 4] 4 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 27]) total number of confs: 18 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237296 none O=C([O-])C1=C(F)C=C(C=C2CC3=C(C=C(Br)S3)C2=O)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 1] 4 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237296 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237296 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237296/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237296 Building REAL300000237297 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237297' /scratch/stefan/7769818/working/building/REAL300000237297 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237297 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237297/0 /scratch/stefan/7769818/working/building/REAL300000237297 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/297 `/scratch/stefan/7769818/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=C(C=C3CC4=C(C=C(Br)S4)C3=O)O2)N1) `REAL300000237297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237297 none O=C([O-])C1=CC2=C(C=C(C=C3CC4=C(C=C(Br)S4)C3=O)O2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 4, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 5] 5 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 28]) total number of confs: 6 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237297 none O=C([O-])C1=CC2=C(C=C(C=C3CC4=C(C=C(Br)S4)C3=O)O2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 4, 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, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237297 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237297 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237297/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237297 Building REAL300000237298 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237298' /scratch/stefan/7769818/working/building/REAL300000237298 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237298 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237298/0 /scratch/stefan/7769818/working/building/REAL300000237298 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/298 `/scratch/stefan/7769818/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC(C=C3CC4=C(C=C(Br)S4)C3=O)=CC=C2O1) `REAL300000237298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237298 none O=C([O-])C1=CC2=CC(C=C3CC4=C(C=C(Br)S4)C3=O)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 29, 30]) total number of confs: 4 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237298 none O=C([O-])C1=CC2=CC(C=C3CC4=C(C=C(Br)S4)C3=O)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1] 3 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237298 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237298 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237298/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237298 Building REAL300000237299 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237299' /scratch/stefan/7769818/working/building/REAL300000237299 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237299 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237299/0 /scratch/stefan/7769818/working/building/REAL300000237299 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/299 `/scratch/stefan/7769818/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2C(C=C3CC4=C(C=C(Br)S4)C3=O)=CC=CN12) `REAL300000237299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237299 none O=C([O-])C1=CN=C2C(C=C3CC4=C(C=C(Br)S4)C3=O)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6] 6 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 28, 29, 30]) total number of confs: 7 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237299 none O=C([O-])C1=CN=C2C(C=C3CC4=C(C=C(Br)S4)C3=O)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1] 6 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 28, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237299 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237299 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237299/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237299 Building REAL300000237300 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237300' /scratch/stefan/7769818/working/building/REAL300000237300 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237300 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237300/0 /scratch/stefan/7769818/working/building/REAL300000237300 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/300 `/scratch/stefan/7769818/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN2C(C=C3CC4=C(C=C(Br)S4)C3=O)=CN=C2C=C1) `REAL300000237300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237300 none O=C([O-])C1=CN2C(C=C3CC4=C(C=C(Br)S4)C3=O)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 7] 7 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 28, 29, 30]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237300 none O=C([O-])C1=CN2C(C=C3CC4=C(C=C(Br)S4)C3=O)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1] 7 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237300 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237300 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237300/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237300 Building REAL300000237301 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237301' /scratch/stefan/7769818/working/building/REAL300000237301 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237301 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237301/0 /scratch/stefan/7769818/working/building/REAL300000237301 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/301 `/scratch/stefan/7769818/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C(C=C2CC3=C(C=C(Br)S3)C2=O)=CC=C1) `REAL300000237301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237301 none O=C([O-])C1=C(F)C(C=C2CC3=C(C=C(Br)S3)C2=O)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1, 1, 1, 7, 7, 7] 7 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 25, 26, 27]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237301 none O=C([O-])C1=C(F)C(C=C2CC3=C(C=C(Br)S3)C2=O)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1] 7 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237301 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237301 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237301/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237301 Building REAL300000237302 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237302' /scratch/stefan/7769818/working/building/REAL300000237302 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237302 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237302/0 /scratch/stefan/7769818/working/building/REAL300000237302 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/302 `/scratch/stefan/7769818/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=C1CC2=C(C=C(Br)S2)C1=O) `REAL300000237302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237302 none COC1=CC(C(=O)[O-])=CC=C1C=C1CC2=C(C=C(Br)S2)C1=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', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', '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, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 5 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27]) total number of confs: 6 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237302 none COC1=CC(C(=O)[O-])=CC=C1C=C1CC2=C(C=C(Br)S2)C1=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', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', '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, 1, 1, 5, 1, 1, 1, 1, 17, 14, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 1, 1, 1, 5, 5, 5, 5] 5 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237302 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237302 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237302/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237302 Building REAL300000237303 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237303' /scratch/stefan/7769818/working/building/REAL300000237303 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237303 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237303/0 /scratch/stefan/7769818/working/building/REAL300000237303 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/303 `/scratch/stefan/7769818/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)C=C1) `REAL300000237303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237303 none O=C([O-])C1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7] 7 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237303 none O=C([O-])C1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 2, 7, 7, 7, 1, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237303 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237303 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237303/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237303 Building REAL300000237304 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237304' /scratch/stefan/7769818/working/building/REAL300000237304 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237304 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237304/0 /scratch/stefan/7769818/working/building/REAL300000237304 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/304 `/scratch/stefan/7769818/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)N=N1) `REAL300000237304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237304 none O=C([O-])CN1C=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 63, 63, 63, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 92, 92, 63, 13, 1, 1, 1] 92 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25]) total number of confs: 263 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237304 none O=C([O-])CN1C=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [16, 8, 16, 1, 1, 1, 1, 1, 10, 10, 10, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 8, 8, 1, 10, 63, 63, 63] 92 rigid atoms, others: [3, 4, 5, 6, 7, 20, 21, 24] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 27, 28]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237304 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237304 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237304/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237304 Building REAL300000237305 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237305' /scratch/stefan/7769818/working/building/REAL300000237305 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237305 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237305/0 /scratch/stefan/7769818/working/building/REAL300000237305 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/305 `/scratch/stefan/7769818/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1) `REAL300000237305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237305 none O=C([O-])C1=CC=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 10, 1, 1, 1, 18] 18 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 21, 22, 23, 24, 25, 29]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237305 none O=C([O-])C1=CC=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 7, 18, 18, 18, 1] 18 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237305 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237305 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237305/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237305 Building REAL300000237306 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237306' /scratch/stefan/7769818/working/building/REAL300000237306 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237306 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237306/0 /scratch/stefan/7769818/working/building/REAL300000237306 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/306 `/scratch/stefan/7769818/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1) `REAL300000237306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237306 none O=C([O-])C1=CSC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 9, 1, 1, 1, 17] 17 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 26]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237306 none O=C([O-])C1=CSC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 7, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237306 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237306 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237306/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237306 Building REAL300000237307 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237307' /scratch/stefan/7769818/working/building/REAL300000237307 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237307 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237307/0 /scratch/stefan/7769818/working/building/REAL300000237307 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/307 `/scratch/stefan/7769818/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=CC=C1O) `REAL300000237307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237307 none O=C([O-])C1=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 12, 1, 1, 1, 28, 28, 56] 56 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237307 none O=C([O-])C1=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 7, 28, 28, 28, 1, 1, 2] 56 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 30]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237307 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237307 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237307/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237307 Building REAL300000237308 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237308' /scratch/stefan/7769818/working/building/REAL300000237308 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237308 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237308/0 /scratch/stefan/7769818/working/building/REAL300000237308 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/308 `/scratch/stefan/7769818/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)C=C1F) `REAL300000237308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237308 none O=C([O-])C1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 8, 1, 1, 1, 17] 17 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237308 none O=C([O-])C1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 7, 17, 17, 17, 1] 17 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237308 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237308 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237308/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237308 Building REAL300000237309 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237309' /scratch/stefan/7769818/working/building/REAL300000237309 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237309 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237309/0 /scratch/stefan/7769818/working/building/REAL300000237309 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/309 `/scratch/stefan/7769818/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)O1) `REAL300000237309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237309 none O=C([O-])C=CC1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 117, 117, 117, 65, 65, 65, 65, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 117, 117, 65, 65, 12, 1, 1, 1] 117 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237309 none O=C([O-])C=CC1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [26, 13, 27, 13, 1, 1, 1, 1, 1, 1, 9, 9, 9, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 13, 13, 1, 1, 9, 65, 65, 65] 117 rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 27, 28, 29, 30]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237309 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237309 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237309/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237309 Building REAL300000237310 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237310' /scratch/stefan/7769818/working/building/REAL300000237310 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237310 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237310/0 /scratch/stefan/7769818/working/building/REAL300000237310 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/310 `/scratch/stefan/7769818/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(F)C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1) `REAL300000237310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237310 none O=C([O-])C1=CC=C(F)C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 9, 1, 1, 1, 17] 17 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 29]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237310 none O=C([O-])C1=CC=C(F)C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 7, 17, 17, 17, 1] 17 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237310 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237310 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237310/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237310 Building REAL300000237311 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237311' /scratch/stefan/7769818/working/building/REAL300000237311 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237311 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237311/0 /scratch/stefan/7769818/working/building/REAL300000237311 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/311 `/scratch/stefan/7769818/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=CC=C1F) `REAL300000237311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237311 none O=C([O-])C1=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 12, 1, 1, 1, 32, 32] 32 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237311 none O=C([O-])C1=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 7, 32, 32, 32, 1, 1] 32 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237311 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237311 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237311/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237311 Building REAL300000237312 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237312' /scratch/stefan/7769818/working/building/REAL300000237312 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237312 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237312/0 /scratch/stefan/7769818/working/building/REAL300000237312 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/312 `/scratch/stefan/7769818/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)C=C1) `REAL300000237312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237312 none O=C([O-])CC1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 17, 17] 17 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 32, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237312 none O=C([O-])CC1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 1, 1] 17 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237312 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237312 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237312/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237312 Building REAL300000237313 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237313' /scratch/stefan/7769818/working/building/REAL300000237313 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237313 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237313/0 /scratch/stefan/7769818/working/building/REAL300000237313 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/313 `/scratch/stefan/7769818/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)S1) `REAL300000237313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237313 none O=C([O-])C1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 14, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 6, 1, 1, 1] 13 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23]) total number of confs: 26 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237313 none O=C([O-])C1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 14, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 3, 13, 13, 13] 13 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237313 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237313 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237313/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237313 Building REAL300000237314 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237314' /scratch/stefan/7769818/working/building/REAL300000237314 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237314 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237314/0 /scratch/stefan/7769818/working/building/REAL300000237314 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/314 `/scratch/stefan/7769818/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)C=N1) `REAL300000237314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237314 none O=C([O-])C1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 7, 1, 1, 1, 13] 13 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 28]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237314 none O=C([O-])C1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 3, 13, 13, 13, 1] 13 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237314 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237314 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237314/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237314 Building REAL300000237315 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237315' /scratch/stefan/7769818/working/building/REAL300000237315 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237315 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237315/0 /scratch/stefan/7769818/working/building/REAL300000237315 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/315 `/scratch/stefan/7769818/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)C=C1O) `REAL300000237315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237315 none O=C([O-])C1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [16, 16, 16, 16, 16, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 8, 1, 1, 1, 16, 32] 32 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237315 none O=C([O-])C1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 7, 16, 16, 16, 1, 2] 32 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 30]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237315 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237315 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237315/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237315 Building REAL300000237316 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237316' /scratch/stefan/7769818/working/building/REAL300000237316 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237316 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237316/0 /scratch/stefan/7769818/working/building/REAL300000237316 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/316 `/scratch/stefan/7769818/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)C=C1C(=O)[O-]) `REAL300000237316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237316 none CC1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 12, 1, 1, 1, 32] 32 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237316 none CC1=CC=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 7, 32, 32, 32, 1] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 18, 19, 20, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237316 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237316 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237316/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237316 Building REAL300000237317 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237317' /scratch/stefan/7769818/working/building/REAL300000237317 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237317 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237317/0 /scratch/stefan/7769818/working/building/REAL300000237317 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/317 `/scratch/stefan/7769818/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)O1) `REAL300000237317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237317 none CC1=C(C(=O)[O-])C=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 13, 1, 1, 1] 32 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 21, 22, 23, 24, 25, 26]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237317 none CC1=C(C(=O)[O-])C=C(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 3, 3, 1, 1, 1, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 2, 2, 2, 1, 8, 32, 32, 32] 32 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 21, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237317 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237317 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237317/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237317 Building REAL300000237318 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237318' /scratch/stefan/7769818/working/building/REAL300000237318 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237318 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237318/0 /scratch/stefan/7769818/working/building/REAL300000237318 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/318 `/scratch/stefan/7769818/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=C(Cl)C1=NC2=CC=C(Br)C=C2O1) `REAL300000237318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237318 none CN1N=C(C(=O)[O-])C=C1C=C(Cl)C1=NC2=CC=C(Br)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 12, 1, 1, 1] 14 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237318 none CN1N=C(C(=O)[O-])C=C1C=C(Cl)C1=NC2=CC=C(Br)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 1, 6, 14, 14, 14] 14 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237318 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237318 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237318/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237318 Building REAL300000237319 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237319' /scratch/stefan/7769818/working/building/REAL300000237319 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237319 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237319/0 /scratch/stefan/7769818/working/building/REAL300000237319 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/319 `/scratch/stefan/7769818/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1) `REAL300000237319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237319 none O=C([O-])C1=CN=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 9, 1, 1, 1, 17] 17 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 21, 22, 23, 24, 28]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237319 none O=C([O-])C1=CN=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 7, 17, 17, 17, 1] 17 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237319 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237319 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237319/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237319 Building REAL300000237320 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237320' /scratch/stefan/7769818/working/building/REAL300000237320 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237320 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237320/0 /scratch/stefan/7769818/working/building/REAL300000237320 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/320 `/scratch/stefan/7769818/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=COC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1) `REAL300000237320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237320 none O=C([O-])C1=COC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 7, 1, 1, 1, 19] 19 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 26]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237320 none O=C([O-])C1=COC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 7, 19, 19, 19, 1] 19 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237320 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237320 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237320/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237320 Building REAL300000237321 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237321' /scratch/stefan/7769818/working/building/REAL300000237321 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237321 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237321/0 /scratch/stefan/7769818/working/building/REAL300000237321 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/321 `/scratch/stefan/7769818/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1) `REAL300000237321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237321 none O=C([O-])CC1=CC=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 20, 20, 10, 20, 20, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 36, 36, 10, 20, 20, 10, 1, 1, 1, 20] 36 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 32, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 158 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237321 none O=C([O-])CC1=CC=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 2, 2, 1, 1, 1, 7, 20, 20, 20, 1] 36 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 22, 25, 26, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 28, 29, 30, 31]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237321 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237321 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237321/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237321 Building REAL300000237322 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237322' /scratch/stefan/7769818/working/building/REAL300000237322 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237322 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237322/0 /scratch/stefan/7769818/working/building/REAL300000237322 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/322 `/scratch/stefan/7769818/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=CS1) `REAL300000237322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237322 none O=C([O-])C1=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 14, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 9, 1, 1, 1, 16] 16 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 8, 19, 20, 21, 22, 26]) total number of confs: 32 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237322 none O=C([O-])C1=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 14, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 7, 16, 16, 16, 1] 16 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237322 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237322 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237322/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237322 Building REAL300000237323 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237323' /scratch/stefan/7769818/working/building/REAL300000237323 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237323 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237323/0 /scratch/stefan/7769818/working/building/REAL300000237323 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/323 `/scratch/stefan/7769818/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1F) `REAL300000237323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237323 none O=C([O-])C1=CC=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 13, 1, 1, 1] 31 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 21, 22, 23, 24, 25, 26]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237323 none O=C([O-])C1=CC=CC(C=C(Cl)C2=NC3=CC=C(Br)C=C3O2)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 17, 1, 1, 12, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 7, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 7, 31, 31, 31] 31 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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 /scratch/stefan/7769818/working/building/REAL300000237323 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237323 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237323/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237323 Building REAL300000237324 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237324' /scratch/stefan/7769818/working/building/REAL300000237324 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237324 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237324/0 /scratch/stefan/7769818/working/building/REAL300000237324 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/324 `/scratch/stefan/7769818/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)=CC=C1OCC(=O)[O-]) `REAL300000237324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237324 none COC1=CC(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 17, 17, 17, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 8, 8, 1, 1, 17, 17, 17, 17, 46, 90, 93, 93, 32, 32, 32, 16, 5, 5, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 17, 17, 90, 90] 201 rigid atoms, others: [34, 35, 7, 9, 10, 11, 12, 13, 43, 18, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 355 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237324 none COC1=CC(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 13, 17, 17, 17, 17, 58, 58, 59, 59, 17, 17, 1, 1, 1, 1, 9, 22, 25, 25, 3, 3, 3, 1, 5, 5, 17, 17, 59, 59, 59, 59, 59, 59, 17, 17, 1, 1, 22, 22] 201 rigid atoms, others: [1, 2, 3, 4, 5, 44, 45, 20, 21, 22, 23, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 241 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237324 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237324 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237324/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237324 Building REAL300000237325 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237325' /scratch/stefan/7769818/working/building/REAL300000237325 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237325 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237325/0 /scratch/stefan/7769818/working/building/REAL300000237325 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/325 `/scratch/stefan/7769818/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000237325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237325 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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 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, 58, 84, 41, 75, 75, 26, 3, 26, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 75, 75, 84, 84, 84, 84, 84, 84, 75, 75, 3, 3, 1, 1, 1, 1, 75, 75] 84 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 320 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237325 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [7, 6, 7, 1, 6, 1, 1, 1, 1, 1, 12, 12, 65, 65, 75, 75, 65, 65, 75, 75, 75, 75, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 65, 65, 75, 75, 75, 75, 1, 1] 84 rigid atoms, others: [3, 5, 6, 7, 8, 9, 39, 22, 23, 38, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 261 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237325 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237325 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237325/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237325 Building REAL300000237326 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237326' /scratch/stefan/7769818/working/building/REAL300000237326 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237326 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237326/0 /scratch/stefan/7769818/working/building/REAL300000237326 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/326 `/scratch/stefan/7769818/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(OCC(=O)[O-])C=C2)C=C1) `REAL300000237326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237326 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(OCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 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, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 44, 87, 21, 44, 44, 11, 3, 11, 3, 1, 1, 1, 1, 1, 1, 6, 18, 34, 34, 1, 1, 44, 44, 87, 87, 87, 87, 87, 87, 44, 44, 3, 3, 1, 1, 18, 18, 1, 1, 44, 44] 201 rigid atoms, others: [36, 37, 40, 41, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 42, 43]) total number of confs: 410 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237326 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(OCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 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, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 11, 29, 29, 44, 44, 29, 29, 119, 180, 187, 187, 44, 44, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 29, 29, 44, 44, 180, 180, 44, 44, 1, 1] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 43, 24, 25] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 621 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237326 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237326 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237326/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237326 Building REAL300000237327 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237327' /scratch/stefan/7769818/working/building/REAL300000237327 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237327 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237327/0 /scratch/stefan/7769818/working/building/REAL300000237327 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/327 `/scratch/stefan/7769818/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(OCCC(=O)[O-])C=C2)C=C1) `REAL300000237327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237327 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(OCCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 52, 90, 20, 52, 52, 12, 3, 12, 3, 1, 1, 1, 1, 1, 1, 6, 14, 15, 23, 23, 1, 1, 52, 52, 90, 90, 90, 90, 90, 90, 52, 52, 3, 3, 1, 1, 14, 14, 14, 14, 1, 1, 52, 52] 201 rigid atoms, others: [37, 38, 44, 43, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 45, 46]) total number of confs: 387 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237327 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(OCCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 12, 12, 37, 37, 52, 52, 37, 37, 161, 188, 188, 192, 192, 52, 52, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 37, 37, 52, 52, 188, 188, 188, 188, 52, 52, 1, 1] 201 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 45, 46, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 499 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237327 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237327 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237327/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237327 Building REAL300000237328 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237328' /scratch/stefan/7769818/working/building/REAL300000237328 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237328 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237328/0 /scratch/stefan/7769818/working/building/REAL300000237328 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/328 `/scratch/stefan/7769818/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CC(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)=C1)C(=O)[O-]) `REAL300000237328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237328 none CC(OC1=CC=CC(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 101, 26, 26, 26, 26, 26, 12, 12, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 8, 8, 1, 1, 26, 142, 143, 143, 142, 142, 142, 142, 26, 26, 26, 12, 12, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 26] 201 rigid atoms, others: [45, 36, 37, 44, 10, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 46]) total number of confs: 398 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237328 none CC(OC1=CC=CC(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 26, 26, 11, 14, 58, 58, 58, 58, 26, 26, 1, 27, 35, 35, 27, 27, 27, 27, 1, 1, 1, 5, 5, 26, 26, 60, 60, 59, 58, 58, 58, 26, 26, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 46, 23, 31] set([0, 1, 9, 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, 41, 42, 43, 44, 45]) total number of confs: 327 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237328 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237328 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237328/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237328 Building REAL300000237329 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237329' /scratch/stefan/7769818/working/building/REAL300000237329 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237329 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237329/0 /scratch/stefan/7769818/working/building/REAL300000237329 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/329 `/scratch/stefan/7769818/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC(OCCC(=O)[O-])=C2)C=C1) `REAL300000237329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237329 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC(OCCC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 77, 86, 19, 77, 12, 43, 43, 12, 6, 12, 6, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 31, 27, 1, 43, 43, 86, 86, 86, 86, 86, 86, 43, 43, 6, 6, 1, 1, 1, 16, 16, 16, 16, 1, 43, 43] 201 rigid atoms, others: [37, 38, 39, 44, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 45, 46]) total number of confs: 404 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237329 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC(OCCC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 10, 21, 21, 43, 43, 43, 43, 43, 133, 170, 170, 183, 178, 43, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 21, 21, 43, 43, 43, 170, 170, 170, 170, 43, 1, 1] 201 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 45, 46, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 470 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237329 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237329 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237329/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237329 Building REAL300000237330 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237330' /scratch/stefan/7769818/working/building/REAL300000237330 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237330 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237330/0 /scratch/stefan/7769818/working/building/REAL300000237330 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/330 `/scratch/stefan/7769818/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)C=C1) `REAL300000237330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237330 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 125, 124, 60, 125, 42, 84, 84, 29, 7, 29, 7, 1, 1, 1, 1, 1, 1, 7, 7, 2, 1, 6, 6, 7, 7, 1, 84, 84, 125, 125, 125, 124, 125, 125, 84, 84, 8, 7, 1, 1, 7, 7, 7, 7, 84, 84] 201 rigid atoms, others: [39, 40, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 481 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237330 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 138, 201, 97, 157, 157, 73, 23, 73, 23, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 157, 157, 201, 201, 201, 201, 201, 201, 157, 157, 23, 23, 7, 7, 1, 1, 1, 1, 157, 157] 201 rigid atoms, others: [41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46]) total number of confs: 741 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: REAL300000237330 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 45, 45, 84, 84, 84, 84, 157, 157, 86, 84, 157, 157, 157, 157, 84, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 45, 45, 84, 84, 157, 157, 157, 157, 1, 1] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 45, 46, 3, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 737 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237330 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237330 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237330/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237330 Building REAL300000237331 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237331' /scratch/stefan/7769818/working/building/REAL300000237331 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237331 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237331/0 /scratch/stefan/7769818/working/building/REAL300000237331 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/331 `/scratch/stefan/7769818/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC(OCC(=O)[O-])=C2)C=C1) `REAL300000237331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237331 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC(OCC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 80, 85, 17, 80, 11, 43, 43, 11, 3, 11, 3, 1, 1, 1, 1, 1, 1, 1, 5, 16, 26, 26, 1, 43, 43, 85, 85, 85, 85, 85, 85, 43, 43, 3, 3, 1, 1, 1, 16, 16, 1, 43, 43] 201 rigid atoms, others: [36, 37, 38, 41, 12, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 42, 43]) total number of confs: 375 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237331 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC(OCC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 11, 11, 28, 28, 43, 43, 43, 43, 43, 101, 159, 166, 166, 43, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 28, 28, 43, 43, 43, 159, 159, 43, 1, 1] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 43, 24, 25] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 524 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237331 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237331 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237331/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237331 Building REAL300000237332 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237332' /scratch/stefan/7769818/working/building/REAL300000237332 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237332 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237332/0 /scratch/stefan/7769818/working/building/REAL300000237332 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/332 `/scratch/stefan/7769818/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)C=C1) `REAL300000237332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237332 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 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, 6, 7, 7, 7, 7, 7, 3, 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: [55, 55, 55, 27, 55, 17, 27, 27, 7, 3, 7, 3, 1, 1, 1, 1, 1, 1, 9, 24, 24, 24, 31, 31, 1, 1, 27, 27, 55, 55, 55, 55, 55, 55, 27, 27, 3, 3, 1, 1, 1, 1, 27, 27] 201 rigid atoms, others: [38, 39, 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, 35, 36, 37, 42, 43]) total number of confs: 289 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237332 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 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, 6, 7, 7, 7, 7, 7, 3, 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: [4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 9, 15, 15, 27, 27, 15, 15, 114, 175, 175, 175, 183, 183, 27, 27, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 15, 15, 27, 27, 27, 27, 1, 1] 201 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 42, 43, 35, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 593 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237332 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237332 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237332/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237332 Building REAL300000237333 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237333' /scratch/stefan/7769818/working/building/REAL300000237333 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237333 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237333/0 /scratch/stefan/7769818/working/building/REAL300000237333 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/333 `/scratch/stefan/7769818/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)C=C1) `REAL300000237333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237333 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [103, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 27, 27, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 11, 11, 1, 1, 80, 80, 103, 103, 103, 80, 27, 27, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 80, 80] 182 rigid atoms, others: [35, 36, 43, 44, 14, 16, 17, 18, 19, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 215 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237333 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 1, 1, 1, 1, 9, 9, 43, 43, 80, 80, 43, 54, 182, 182, 182, 182, 80, 80, 1, 1, 3, 3, 3, 1, 9, 9, 80, 80, 182, 182, 182, 182, 182, 182, 80, 80, 1, 1] 182 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 45, 46, 27, 28] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 590 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237333 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237333 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237333/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237333 Building REAL300000237334 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237334' /scratch/stefan/7769818/working/building/REAL300000237334 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237334 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237334/0 /scratch/stefan/7769818/working/building/REAL300000237334 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/334 `/scratch/stefan/7769818/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CN(CC(=O)[O-])N=N2)C=C1) `REAL300000237334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237334 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CN(CC(=O)[O-])N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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: [171, 162, 171, 30, 161, 30, 104, 104, 30, 9, 29, 9, 1, 1, 1, 1, 1, 6, 9, 9, 1, 1, 104, 104, 171, 171, 171, 171, 171, 171, 104, 104, 9, 9, 1, 6, 6, 104, 104] 201 rigid atoms, others: [34, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 655 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237334 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CN(CC(=O)[O-])N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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: [6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 47, 47, 104, 104, 104, 160, 165, 165, 104, 104, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 47, 47, 104, 160, 160, 1, 1] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 22, 23, 38, 37, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 536 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237334 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237334 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237334/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237334 Building REAL300000237335 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237335' /scratch/stefan/7769818/working/building/REAL300000237335 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237335 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237335/0 /scratch/stefan/7769818/working/building/REAL300000237335 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/335 `/scratch/stefan/7769818/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2)C=C1) `REAL300000237335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237335 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 97, 201, 97, 164, 164, 47, 6, 47, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 164, 164, 201, 201, 201, 201, 201, 201, 164, 164, 6, 6, 1, 1, 1, 1, 164, 164] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 732 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237335 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 10, 1, 6, 1, 1, 1, 1, 1, 12, 12, 81, 81, 164, 164, 164, 164, 164, 164, 164, 164, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1, 81, 81, 164, 164, 164, 164, 1, 1] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 39, 22, 23, 38, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 349 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237335 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237335 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237335/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237335 Building REAL300000237336 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237336' /scratch/stefan/7769818/working/building/REAL300000237336 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237336 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237336/0 /scratch/stefan/7769818/working/building/REAL300000237336 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/336 `/scratch/stefan/7769818/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(C(=O)[O-])=CS2)C=C1) `REAL300000237336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237336 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(C(=O)[O-])=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 144, 201, 108, 158, 158, 71, 12, 70, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 158, 158, 201, 201, 201, 201, 201, 201, 158, 158, 12, 12, 1, 1, 158, 158] 201 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 646 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237336 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(C(=O)[O-])=CS2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 55, 55, 158, 158, 158, 158, 158, 158, 158, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 55, 55, 158, 158, 1, 1] 201 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 35, 21, 22, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 297 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237336 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237336 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237336/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237336 Building REAL300000237337 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237337' /scratch/stefan/7769818/working/building/REAL300000237337 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237337 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237337/0 /scratch/stefan/7769818/working/building/REAL300000237337 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/337 `/scratch/stefan/7769818/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)=CC=C1OCCC(=O)[O-]) `REAL300000237337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237337 none COC1=CC(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 27, 27, 27, 27, 112, 136, 136, 158, 156, 46, 46, 46, 26, 9, 9, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 27, 27, 136, 136, 136, 136] 201 rigid atoms, others: [35, 36, 7, 9, 10, 11, 12, 13, 44, 43, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50]) total number of confs: 428 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237337 none COC1=CC(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 27, 27, 17, 27, 45, 45, 45, 45, 27, 27, 1, 1, 1, 1, 9, 21, 21, 35, 31, 3, 3, 3, 1, 5, 5, 27, 27, 45, 45, 45, 45, 45, 45, 27, 27, 1, 1, 21, 21, 21, 21] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 45, 46, 20, 21, 22, 23] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 298 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237337 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237337 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237337/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237337 Building REAL300000237338 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237338' /scratch/stefan/7769818/working/building/REAL300000237338 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237338 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237338/0 /scratch/stefan/7769818/working/building/REAL300000237338 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/338 `/scratch/stefan/7769818/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2Cl)C=C1) `REAL300000237338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237338 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 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, 6, 7, 7, 7, 7, 7, 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 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 200, 98, 199, 62, 158, 158, 62, 9, 62, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 158, 158, 200, 200, 200, 200, 200, 200, 158, 158, 9, 9, 1, 1, 1, 158, 158] 200 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 819 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237338 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 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, 6, 7, 7, 7, 7, 7, 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 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 79, 79, 158, 158, 90, 141, 158, 158, 158, 158, 158, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 79, 79, 158, 158, 158, 1, 1] 200 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 39, 23, 24, 38, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 635 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237338 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237338 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237338/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237338 Building REAL300000237339 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237339' /scratch/stefan/7769818/working/building/REAL300000237339 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237339 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237339/0 /scratch/stefan/7769818/working/building/REAL300000237339 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/339 `/scratch/stefan/7769818/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2Cl)C=C1) `REAL300000237339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237339 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 139, 201, 100, 144, 144, 53, 9, 53, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 144, 144, 201, 201, 201, 201, 201, 201, 144, 144, 9, 9, 1, 1, 1, 144, 144] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 627 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237339 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 55, 55, 144, 144, 144, 144, 144, 148, 148, 144, 144, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 55, 55, 144, 144, 144, 1, 1] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 39, 23, 24, 38, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 298 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237339 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237339 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237339/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237339 Building REAL300000237340 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237340' /scratch/stefan/7769818/working/building/REAL300000237340 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237340 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237340/0 /scratch/stefan/7769818/working/building/REAL300000237340 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/340 `/scratch/stefan/7769818/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(O)C(C(=O)[O-])=C2)C=C1) `REAL300000237340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237340 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(O)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 172, 201, 96, 172, 172, 45, 5, 45, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 172, 172, 201, 201, 201, 201, 201, 201, 172, 172, 5, 5, 1, 1, 2, 1, 172, 172] 402 rigid atoms, others: [35, 36, 38, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 39, 40]) total number of confs: 669 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237340 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(O)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 88, 88, 172, 172, 172, 172, 172, 172, 172, 172, 172, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 88, 88, 172, 172, 344, 172, 1, 1] 402 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 39, 40, 23, 24, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 690 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237340 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237340 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237340/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237340 Building REAL300000237341 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237341' /scratch/stefan/7769818/working/building/REAL300000237341 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237341 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237341/0 /scratch/stefan/7769818/working/building/REAL300000237341 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/341 `/scratch/stefan/7769818/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(C(=O)N(C)C)C=C1) `REAL300000237341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237341 none CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(C(=O)N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 44, 44, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 11, 11, 1, 1, 99, 99, 99, 99, 99, 99, 99, 99, 44, 44, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1] 137 rigid atoms, others: [45, 36, 37, 44, 13, 15, 16, 17, 18, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 213 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237341 none CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(C(=O)N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 53, 53, 99, 99, 53, 65, 137, 137, 137, 137, 99, 99, 2, 2, 2, 1, 2, 2, 2, 1, 9, 9, 99, 99, 137, 137, 137, 137, 137, 137, 99, 99] 137 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 29] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 551 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237341 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237341 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237341/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237341 Building REAL300000237342 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237342' /scratch/stefan/7769818/working/building/REAL300000237342 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237342 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237342/0 /scratch/stefan/7769818/working/building/REAL300000237342 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/342 `/scratch/stefan/7769818/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)C=C1)C(=O)[O-]) `REAL300000237342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237342 none CC(OC1=CC=C(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 118, 44, 23, 68, 68, 23, 23, 7, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 68, 68, 163, 167, 167, 163, 163, 163, 163, 68, 68, 23, 23, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 68, 68] 201 rigid atoms, others: [35, 36, 9, 11, 12, 13, 14, 15, 43, 20, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 618 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237342 none CC(OC1=CC=C(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 6, 6, 31, 32, 68, 68, 32, 32, 111, 111, 111, 111, 68, 68, 1, 1, 13, 19, 19, 13, 13, 13, 13, 1, 1, 6, 6, 68, 68, 111, 111, 111, 111, 111, 111, 68, 68, 1, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 45, 46, 22, 23, 31] set([0, 1, 8, 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, 40, 41, 42, 43, 44]) total number of confs: 444 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237342 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237342 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237342/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237342 Building REAL300000237343 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237343' /scratch/stefan/7769818/working/building/REAL300000237343 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237343 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237343/0 /scratch/stefan/7769818/working/building/REAL300000237343 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/343 `/scratch/stefan/7769818/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC=C2OCCC(=O)[O-])C=C1) `REAL300000237343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237343 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC=C2OCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 84, 104, 22, 84, 22, 64, 64, 22, 7, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 31, 38, 65, 57, 64, 64, 104, 104, 104, 104, 104, 104, 64, 64, 7, 7, 1, 1, 1, 1, 31, 31, 38, 38, 64, 64] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46]) total number of confs: 638 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237343 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC=C2OCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 10, 10, 38, 38, 64, 64, 43, 64, 64, 64, 143, 178, 181, 189, 183, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 38, 38, 64, 64, 64, 64, 178, 178, 181, 181, 1, 1] 201 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 45, 46, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 602 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237343 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237343 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237343/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237343 Building REAL300000237344 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237344' /scratch/stefan/7769818/working/building/REAL300000237344 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237344 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237344/0 /scratch/stefan/7769818/working/building/REAL300000237344 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/344 `/scratch/stefan/7769818/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=C(C(=O)[O-])C=NN2C)C=C1) `REAL300000237344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237344 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=C(C(=O)[O-])C=NN2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 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, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [137, 123, 137, 42, 123, 40, 78, 78, 25, 9, 25, 9, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 78, 78, 137, 137, 137, 137, 137, 137, 78, 78, 9, 9, 1, 2, 2, 2, 78, 78] 137 rigid atoms, others: [34, 12, 13, 14, 15, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 496 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237344 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=C(C(=O)[O-])C=NN2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 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, 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: [8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 44, 44, 78, 78, 88, 88, 78, 78, 78, 78, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 44, 44, 78, 78, 78, 78, 1, 1] 137 rigid atoms, others: [3, 5, 6, 7, 8, 9, 39, 22, 23, 38, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 222 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237344 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237344 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237344/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237344 Building REAL300000237345 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237345' /scratch/stefan/7769818/working/building/REAL300000237345 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237345 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237345/0 /scratch/stefan/7769818/working/building/REAL300000237345 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/345 `/scratch/stefan/7769818/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1) `REAL300000237345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237345 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 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, 6, 7, 7, 7, 7, 7, 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: [201, 201, 201, 133, 201, 88, 133, 133, 43, 5, 43, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 133, 133, 201, 201, 201, 201, 201, 201, 133, 133, 5, 5, 1, 1, 1, 133, 133] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 637 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237345 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 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, 6, 7, 7, 7, 7, 7, 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: [6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 60, 60, 133, 133, 133, 133, 174, 174, 133, 133, 133, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 60, 60, 133, 133, 133, 1, 1] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 39, 23, 24, 38, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 431 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237345 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237345 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237345/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237345 Building REAL300000237346 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237346' /scratch/stefan/7769818/working/building/REAL300000237346 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237346 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237346/0 /scratch/stefan/7769818/working/building/REAL300000237346 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/346 `/scratch/stefan/7769818/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C=CC(=O)[O-])O2)C=C1) `REAL300000237346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237346 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C=CC(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 141, 151, 54, 141, 50, 92, 92, 28, 8, 27, 8, 1, 1, 1, 1, 1, 1, 12, 12, 30, 30, 1, 92, 92, 159, 159, 159, 151, 151, 151, 92, 92, 8, 8, 1, 1, 12, 12, 92, 92] 201 rigid atoms, others: [35, 36, 12, 13, 14, 15, 16, 17, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 602 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237346 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C=CC(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 51, 51, 92, 92, 92, 92, 162, 162, 179, 179, 92, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 51, 51, 92, 92, 162, 162, 1, 1] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 39, 40, 23, 24, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 493 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237346 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237346 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237346/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237346 Building REAL300000237347 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237347' /scratch/stefan/7769818/working/building/REAL300000237347 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237347 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237347/0 /scratch/stefan/7769818/working/building/REAL300000237347 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/347 `/scratch/stefan/7769818/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)C=C1C(=O)[O-]) `REAL300000237347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237347 none COC1=CC=C(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)C=C1C(=O)[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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 61, 61, 61, 26, 26, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 11, 11, 1, 1, 61, 61, 61, 78, 78, 106, 106, 106, 61, 61, 26, 26, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 60] 201 rigid atoms, others: [33, 34, 8, 41, 10, 11, 12, 13, 14, 19, 20, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 303 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237347 none COC1=CC=C(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)C=C1C(=O)[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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 61, 61, 31, 61, 189, 189, 192, 192, 61, 61, 1, 1, 1, 3, 3, 4, 4, 4, 1, 1, 5, 5, 61, 61, 192, 192, 192, 192, 192, 192, 61, 61, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 43, 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, 41, 42]) total number of confs: 615 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237347 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237347 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237347/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237347 Building REAL300000237348 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237348' /scratch/stefan/7769818/working/building/REAL300000237348 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237348 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237348/0 /scratch/stefan/7769818/working/building/REAL300000237348 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/348 `/scratch/stefan/7769818/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(C(=O)[O-])=CC=C2F)C=C1) `REAL300000237348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237348 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(C(=O)[O-])=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 117, 201, 118, 159, 159, 59, 11, 59, 11, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 159, 159, 201, 201, 201, 201, 201, 201, 159, 159, 11, 11, 1, 1, 1, 159, 159] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 626 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237348 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(C(=O)[O-])=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 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, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 49, 49, 159, 159, 159, 159, 159, 159, 159, 159, 159, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 49, 49, 159, 159, 159, 1, 1] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 39, 23, 24, 38, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 289 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237348 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237348 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237348/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237348 Building REAL300000237349 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237349' /scratch/stefan/7769818/working/building/REAL300000237349 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237349 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237349/0 /scratch/stefan/7769818/working/building/REAL300000237349 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/349 `/scratch/stefan/7769818/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(C(=O)N(C)C)C=C1) `REAL300000237349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237349 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(C(=O)N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 77, 77, 77, 77, 77, 113, 77, 77, 102, 102, 77, 26, 26, 7, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 108, 108, 108, 77, 113, 113, 113, 77, 26, 26, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1] 201 rigid atoms, others: [38, 39, 47, 46, 15, 17, 18, 19, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 365 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237349 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(C(=O)N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 3, 3, 1, 1, 1, 9, 9, 38, 38, 77, 77, 38, 38, 115, 115, 115, 115, 77, 77, 4, 4, 4, 1, 3, 3, 3, 1, 9, 9, 77, 77, 115, 115, 115, 115, 115, 115, 77, 77] 201 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 11, 12, 13, 35, 31] set([0, 6, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 437 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237349 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237349 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237349/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237349 Building REAL300000237350 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237350' /scratch/stefan/7769818/working/building/REAL300000237350 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237350 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237350/0 /scratch/stefan/7769818/working/building/REAL300000237350 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/350 `/scratch/stefan/7769818/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(F)C(C(=O)[O-])=C2)C=C1) `REAL300000237350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237350 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 6, 7, 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, 7, 7, 7] 0 hydrogens 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, 140, 201, 89, 140, 140, 42, 5, 42, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 140, 140, 201, 201, 201, 201, 201, 201, 140, 140, 5, 5, 1, 1, 1, 140, 140] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 639 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237350 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(F)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 6, 7, 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, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 58, 58, 140, 140, 140, 140, 140, 140, 169, 169, 140, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 58, 58, 140, 140, 140, 1, 1] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 39, 23, 24, 38, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 392 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237350 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237350 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237350/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237350 Building REAL300000237351 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237351' /scratch/stefan/7769818/working/building/REAL300000237351 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237351 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237351/0 /scratch/stefan/7769818/working/building/REAL300000237351 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/351 `/scratch/stefan/7769818/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(CC(=O)[O-])C=C2)C=C1) `REAL300000237351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237351 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 174, 174, 104, 174, 48, 104, 104, 25, 3, 25, 3, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 104, 104, 174, 174, 174, 174, 174, 174, 104, 104, 3, 3, 1, 1, 2, 2, 1, 1, 104, 104] 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, 42]) total number of confs: 581 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237351 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 6, 1, 1, 1, 1, 1, 12, 12, 80, 80, 104, 104, 80, 104, 154, 180, 180, 104, 104, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 80, 80, 104, 104, 154, 154, 104, 104, 1, 1] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 42, 41, 23, 24, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 775 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237351 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237351 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237351/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237351 Building REAL300000237352 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237352' /scratch/stefan/7769818/working/building/REAL300000237352 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237352 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237352/0 /scratch/stefan/7769818/working/building/REAL300000237352 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/352 `/scratch/stefan/7769818/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])S2)C=C1) `REAL300000237352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237352 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [183, 183, 183, 118, 183, 71, 156, 156, 71, 13, 71, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 156, 156, 183, 183, 183, 183, 183, 183, 156, 156, 13, 13, 1, 1, 156, 156] 183 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 730 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237352 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 52, 52, 156, 156, 156, 156, 156, 156, 156, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 52, 52, 156, 156, 1, 1] 183 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 35, 21, 22, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 290 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237352 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237352 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237352/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237352 Building REAL300000237353 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237353' /scratch/stefan/7769818/working/building/REAL300000237353 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237353 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237353/0 /scratch/stefan/7769818/working/building/REAL300000237353 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/353 `/scratch/stefan/7769818/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C=CC(=O)[O-])C=C2)C=C1) `REAL300000237353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237353 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C=CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 169, 169, 102, 169, 49, 102, 102, 23, 3, 23, 3, 1, 1, 1, 1, 1, 1, 5, 5, 23, 23, 1, 1, 102, 102, 169, 169, 169, 169, 169, 169, 102, 102, 3, 3, 1, 1, 5, 5, 1, 1, 102, 102] 201 rigid atoms, others: [36, 37, 40, 41, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 42, 43]) total number of confs: 599 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237353 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C=CC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 71, 71, 102, 102, 71, 71, 164, 164, 185, 185, 102, 102, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 71, 71, 102, 102, 164, 164, 102, 102, 1, 1] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 42, 43, 24, 25] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 688 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237353 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237353 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237353/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237353 Building REAL300000237354 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237354' /scratch/stefan/7769818/working/building/REAL300000237354 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237354 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237354/0 /scratch/stefan/7769818/working/building/REAL300000237354 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/354 `/scratch/stefan/7769818/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(F)=C(C(=O)[O-])C=C2F)C=C1) `REAL300000237354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237354 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(F)=C(C(=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 170, 201, 45, 170, 45, 139, 139, 45, 11, 45, 11, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 139, 139, 201, 201, 201, 201, 201, 201, 139, 139, 11, 11, 1, 1, 139, 139] 201 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 799 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237354 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(F)=C(C(=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 46, 46, 139, 139, 139, 139, 139, 176, 176, 139, 139, 139, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 46, 46, 139, 139, 1, 1] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 39, 24, 25, 38] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 407 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237354 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237354 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237354/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237354 Building REAL300000237355 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237355' /scratch/stefan/7769818/working/building/REAL300000237355 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237355 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237355/0 /scratch/stefan/7769818/working/building/REAL300000237355 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/355 `/scratch/stefan/7769818/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=C3C(=CC=C2)NN=C3C(=O)[O-])C=C1) `REAL300000237355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237355 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=C3C(=CC=C2)NN=C3C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 71, 78, 24, 71, 24, 62, 62, 24, 8, 24, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 62, 62, 78, 78, 78, 78, 78, 78, 62, 62, 8, 8, 1, 1, 1, 1, 62, 62] 78 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 329 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237355 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=C3C(=CC=C2)NN=C3C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 37, 37, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 37, 37, 62, 62, 62, 62, 1, 1] 78 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 42, 41, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237355 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237355 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237355/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237355 Building REAL300000237356 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237356' /scratch/stefan/7769818/working/building/REAL300000237356 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237356 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237356/0 /scratch/stefan/7769818/working/building/REAL300000237356 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/356 `/scratch/stefan/7769818/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1) `REAL300000237356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237356 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', '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', '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, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [130, 130, 130, 93, 130, 67, 93, 93, 27, 4, 27, 4, 1, 1, 1, 1, 1, 1, 3, 3, 1, 2, 3, 3, 3, 3, 1, 1, 93, 93, 130, 130, 130, 128, 130, 130, 93, 93, 4, 4, 1, 1, 3, 3, 3, 3, 1, 1, 93, 93] 156 rigid atoms, others: [47, 40, 41, 12, 13, 14, 15, 16, 17, 46, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 48, 49]) total number of confs: 407 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237356 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', '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', '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, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [156, 156, 156, 131, 156, 109, 131, 131, 48, 7, 48, 7, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 131, 131, 156, 156, 156, 156, 156, 156, 131, 131, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 131, 131] 156 rigid atoms, others: [42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49]) total number of confs: 436 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: REAL300000237356 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', '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', '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, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 79, 79, 93, 93, 79, 91, 131, 131, 93, 93, 131, 131, 131, 131, 93, 93, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 79, 79, 93, 93, 131, 131, 131, 131, 93, 93, 1, 1] 156 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 48, 49, 28, 29, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 640 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237356 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237356 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237356/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237356 Building REAL300000237357 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237357' /scratch/stefan/7769818/working/building/REAL300000237357 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237357 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237357/0 /scratch/stefan/7769818/working/building/REAL300000237357 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/357 `/scratch/stefan/7769818/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CNC3=CC=C(C(=O)[O-])C=C23)C=C1) `REAL300000237357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237357 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CNC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 192, 110, 192, 78, 144, 144, 53, 12, 53, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 144, 144, 192, 192, 192, 192, 192, 192, 144, 144, 12, 12, 1, 1, 1, 1, 1, 144, 144] 192 rigid atoms, others: [37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43]) total number of confs: 708 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237357 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CNC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 49, 49, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 144, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 49, 49, 144, 144, 144, 144, 144, 1, 1] 192 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 42, 43, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 266 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237357 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237357 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237357/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237357 Building REAL300000237358 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237358' /scratch/stefan/7769818/working/building/REAL300000237358 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237358 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237358/0 /scratch/stefan/7769818/working/building/REAL300000237358 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/358 `/scratch/stefan/7769818/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])N=C2)C=C1) `REAL300000237358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237358 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 103, 168, 83, 141, 141, 52, 6, 52, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 141, 141, 168, 168, 168, 168, 168, 168, 141, 141, 6, 6, 1, 1, 1, 141, 141] 168 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 611 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237358 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])N=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 1, 6, 1, 1, 1, 1, 1, 12, 12, 84, 84, 141, 141, 141, 141, 141, 141, 141, 141, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 84, 84, 141, 141, 141, 1, 1] 168 rigid atoms, others: [3, 5, 6, 7, 8, 9, 22, 23, 38, 37, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 314 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237358 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237358 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237358/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237358 Building REAL300000237359 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237359' /scratch/stefan/7769818/working/building/REAL300000237359 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237359 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237359/0 /scratch/stefan/7769818/working/building/REAL300000237359 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/359 `/scratch/stefan/7769818/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])C(O)=C2)C=C1) `REAL300000237359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237359 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])C(O)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 144, 201, 86, 144, 144, 45, 5, 45, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 144, 144, 201, 201, 201, 201, 201, 201, 144, 144, 5, 5, 1, 1, 2, 1, 144, 144] 402 rigid atoms, others: [35, 36, 38, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 39, 40]) total number of confs: 655 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237359 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])C(O)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 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: [6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 73, 73, 144, 144, 144, 144, 171, 171, 144, 144, 144, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 73, 73, 144, 144, 288, 144, 1, 1] 402 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 39, 40, 23, 24, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 692 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237359 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237359 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237359/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237359 Building REAL300000237360 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237360' /scratch/stefan/7769818/working/building/REAL300000237360 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237360 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237360/0 /scratch/stefan/7769818/working/building/REAL300000237360 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/360 `/scratch/stefan/7769818/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)C=C1C(=O)[O-]) `REAL300000237360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237360 none CC1=CC=C(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [89, 89, 89, 89, 39, 39, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 13, 13, 1, 1, 89, 89, 89, 129, 129, 89, 89, 89, 89, 89, 39, 39, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1, 89] 189 rigid atoms, others: [32, 33, 7, 40, 9, 10, 11, 12, 13, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 359 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237360 none CC1=CC=C(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 37, 37, 89, 89, 37, 37, 181, 181, 189, 185, 89, 89, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 5, 5, 89, 89, 189, 189, 189, 188, 185, 185, 89, 89, 1] 189 rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 20, 21, 22, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 647 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237360 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237360 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237360/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237360 Building REAL300000237361 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237361' /scratch/stefan/7769818/working/building/REAL300000237361 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237361 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237361/0 /scratch/stefan/7769818/working/building/REAL300000237361 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/361 `/scratch/stefan/7769818/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(C(=O)[O-])=C(Cl)S2)C=C1) `REAL300000237361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237361 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(C(=O)[O-])=C(Cl)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 98, 201, 78, 133, 133, 37, 13, 36, 13, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 133, 133, 201, 201, 201, 199, 201, 201, 133, 133, 13, 13, 1, 133, 133] 201 rigid atoms, others: [34, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 726 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237361 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(C(=O)[O-])=C(Cl)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 32, 32, 133, 133, 133, 166, 166, 133, 133, 133, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 32, 32, 133, 1, 1] 201 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 35, 22, 23, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 348 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237361 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237361 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237361/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237361 Building REAL300000237362 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237362' /scratch/stefan/7769818/working/building/REAL300000237362 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237362 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237362/0 /scratch/stefan/7769818/working/building/REAL300000237362 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/362 `/scratch/stefan/7769818/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)O1) `REAL300000237362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237362 none CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 65, 65, 51, 21, 21, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 9, 9, 1, 1, 51, 51, 51, 51, 51, 21, 21, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1] 88 rigid atoms, others: [38, 39, 10, 12, 13, 14, 15, 16, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 176 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237362 none CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 12, 12, 29, 29, 51, 51, 29, 39, 88, 88, 88, 88, 51, 51, 1, 2, 2, 2, 1, 12, 12, 51, 51, 88, 88, 88, 88, 88, 88, 51, 51] 88 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 23, 27] set([4, 5, 9, 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, 38, 39]) total number of confs: 328 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237362 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237362 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237362/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237362 Building REAL300000237363 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237363' /scratch/stefan/7769818/working/building/REAL300000237363 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237363 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237363/0 /scratch/stefan/7769818/working/building/REAL300000237363 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/363 `/scratch/stefan/7769818/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(C(=O)[O-])=NN2C)C=C1) `REAL300000237363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237363 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(C(=O)[O-])=NN2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 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, 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, 117, 184, 97, 143, 143, 61, 10, 61, 10, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 143, 143, 184, 184, 184, 184, 184, 184, 143, 143, 10, 10, 1, 2, 2, 2, 143, 143] 184 rigid atoms, others: [34, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 627 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237363 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(C(=O)[O-])=NN2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 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, 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: [8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 58, 58, 143, 143, 143, 143, 143, 143, 143, 143, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 58, 58, 143, 143, 143, 143, 1, 1] 184 rigid atoms, others: [3, 5, 6, 7, 8, 9, 39, 22, 23, 38, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 282 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237363 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237363 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237363/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237363 Building REAL300000237364 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237364' /scratch/stefan/7769818/working/building/REAL300000237364 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237364 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237364/0 /scratch/stefan/7769818/working/building/REAL300000237364 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/364 `/scratch/stefan/7769818/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CN=CC(C(=O)[O-])=C2)C=C1) `REAL300000237364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237364 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CN=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 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, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 97, 201, 70, 163, 163, 43, 6, 43, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 163, 163, 201, 201, 201, 201, 201, 201, 163, 163, 6, 6, 1, 1, 1, 163, 163] 201 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 773 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237364 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CN=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 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, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 6, 10, 1, 6, 1, 1, 1, 1, 1, 12, 12, 80, 80, 163, 163, 163, 163, 163, 163, 163, 163, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1, 80, 80, 163, 163, 163, 1, 1] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 22, 23, 38, 37, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 342 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237364 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237364 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237364/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237364 Building REAL300000237365 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237365' /scratch/stefan/7769818/working/building/REAL300000237365 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237365 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237365/0 /scratch/stefan/7769818/working/building/REAL300000237365 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/365 `/scratch/stefan/7769818/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(C(=O)[O-])=CO2)C=C1) `REAL300000237365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237365 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(C(=O)[O-])=CO2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 6, 7, 7, 7, 7, 7, 3, 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 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, 81, 108, 81, 81, 81, 37, 10, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 108, 108, 108, 108, 108, 108, 81, 81, 10, 10, 1, 1, 81, 81] 108 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 253 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237365 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(C(=O)[O-])=CO2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 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, 6, 7, 7, 7, 7, 7, 3, 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 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 51, 51, 81, 81, 81, 81, 81, 81, 81, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 51, 51, 81, 81, 1, 1] 108 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 35, 21, 22, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 195 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237365 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237365 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237365/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237365 Building REAL300000237366 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237366' /scratch/stefan/7769818/working/building/REAL300000237366 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237366 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237366/0 /scratch/stefan/7769818/working/building/REAL300000237366 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/366 `/scratch/stefan/7769818/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(C(=O)N(C)C)C=C1) `REAL300000237366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237366 none COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(C(=O)N(C)C)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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 98, 98, 98, 98, 98, 98, 98, 98, 98, 26, 26, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 11, 11, 1, 1, 113, 113, 113, 98, 98, 98, 26, 26, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1] 201 rigid atoms, others: [34, 35, 42, 43, 13, 15, 16, 17, 18, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 217 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237366 none COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(C(=O)N(C)C)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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 9, 9, 52, 52, 98, 98, 52, 52, 193, 193, 193, 193, 98, 98, 4, 4, 4, 1, 1, 1, 9, 9, 98, 98, 194, 193, 193, 193, 193, 193, 98, 98] 201 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, 41, 42, 43]) total number of confs: 639 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237366 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237366 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237366/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237366 Building REAL300000237367 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237367' /scratch/stefan/7769818/working/building/REAL300000237367 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237367 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237367/0 /scratch/stefan/7769818/working/building/REAL300000237367 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/367 `/scratch/stefan/7769818/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C=C1) `REAL300000237367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237367 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 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, 118, 138, 80, 118, 118, 36, 9, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 118, 118, 138, 138, 138, 138, 138, 138, 118, 118, 9, 9, 1, 1, 1, 1, 118, 118] 138 rigid atoms, others: [37, 38, 39, 40, 12, 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, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 439 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237367 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 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: [8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 48, 48, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 48, 48, 118, 118, 118, 118, 1, 1] 138 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 42, 41, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 230 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237367 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237367 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237367/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237367 Building REAL300000237368 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237368' /scratch/stefan/7769818/working/building/REAL300000237368 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237368 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237368/0 /scratch/stefan/7769818/working/building/REAL300000237368 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/368 `/scratch/stefan/7769818/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2[N+](=O)[O-])C=C1) `REAL300000237368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237368 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2[N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 186, 89, 186, 64, 126, 126, 41, 5, 41, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 126, 126, 186, 186, 186, 186, 186, 186, 126, 126, 5, 5, 1, 1, 1, 126, 126] 186 rigid atoms, others: [37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41]) total number of confs: 677 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237368 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C(=O)[O-])C=C2[N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 3, 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] 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: [8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 68, 68, 126, 126, 68, 73, 126, 126, 126, 126, 126, 126, 126, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 68, 68, 126, 126, 126, 1, 1] 186 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 40, 41, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 593 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237368 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237368 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237368/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237368 Building REAL300000237369 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237369' /scratch/stefan/7769818/working/building/REAL300000237369 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237369 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237369/0 /scratch/stefan/7769818/working/building/REAL300000237369 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/369 `/scratch/stefan/7769818/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC(CC(=O)[O-])=C2)C=C1) `REAL300000237369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237369 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 158, 162, 79, 158, 41, 122, 122, 37, 5, 37, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 122, 122, 163, 164, 164, 162, 162, 162, 122, 122, 5, 5, 1, 1, 1, 2, 2, 1, 122, 122] 201 rigid atoms, others: [35, 36, 37, 40, 12, 13, 14, 15, 16, 17, 18, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 41, 42]) total number of confs: 661 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237369 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC(CC(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 54, 54, 122, 122, 54, 122, 122, 172, 180, 180, 122, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 54, 54, 122, 122, 54, 172, 172, 122, 1, 1] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 42, 41, 23, 24, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 731 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237369 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237369 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237369/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237369 Building REAL300000237370 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237370' /scratch/stefan/7769818/working/building/REAL300000237370 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237370 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237370/0 /scratch/stefan/7769818/working/building/REAL300000237370 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/370 `/scratch/stefan/7769818/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)=CC=C1C(=O)[O-]) `REAL300000237370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237370 none COC1=CC(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [46, 27, 27, 27, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 11, 11, 1, 1, 27, 27, 27, 27, 44, 44, 46, 46, 46, 27, 10, 10, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 27, 27] 111 rigid atoms, others: [32, 33, 7, 40, 9, 10, 11, 12, 13, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 42, 43]) total number of confs: 187 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237370 none COC1=CC(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 9, 9, 27, 27, 11, 27, 76, 76, 80, 80, 27, 27, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 5, 5, 27, 27, 80, 80, 80, 80, 80, 80, 27, 27, 1, 1] 111 rigid atoms, others: [1, 2, 3, 4, 5, 42, 43, 20, 21, 22, 23, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 282 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237370 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237370 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237370/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237370 Building REAL300000237371 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237371' /scratch/stefan/7769818/working/building/REAL300000237371 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237371 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237371/0 /scratch/stefan/7769818/working/building/REAL300000237371 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/371 `/scratch/stefan/7769818/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=C(F)C=C(C(=O)[O-])C=C2F)C=C1) `REAL300000237371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237371 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=C(F)C=C(C(=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 103, 128, 83, 103, 103, 40, 7, 40, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 103, 103, 128, 128, 128, 128, 128, 128, 103, 103, 7, 7, 1, 1, 103, 103] 128 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 380 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237371 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=C(F)C=C(C(=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 9, 1, 6, 1, 1, 1, 1, 1, 12, 12, 91, 91, 156, 156, 156, 91, 91, 156, 156, 156, 156, 156, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 91, 91, 156, 156, 1, 1] 175 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 39, 24, 25, 38] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 744 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237371 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237371 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237371/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237371 Building REAL300000237372 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237372' /scratch/stefan/7769818/working/building/REAL300000237372 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237372 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237372/0 /scratch/stefan/7769818/working/building/REAL300000237372 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/372 `/scratch/stefan/7769818/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=C(F)C=CC(C(=O)[O-])=C2F)C=C1) `REAL300000237372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237372 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=C(F)C=CC(C(=O)[O-])=C2F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 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, 7, 7, 7] 0 hydrogens 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, 198, 201, 94, 198, 72, 140, 140, 47, 11, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 140, 140, 201, 201, 201, 201, 201, 201, 140, 140, 11, 11, 1, 1, 140, 140] 201 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 717 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237372 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=C(F)C=CC(C(=O)[O-])=C2F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 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, 7, 7, 7] 0 hydrogens 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, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 41, 41, 140, 140, 140, 140, 140, 140, 168, 168, 140, 140, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 41, 41, 140, 140, 1, 1] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 39, 24, 25, 38] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 366 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237372 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237372 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237372/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237372 Building REAL300000237373 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237373' /scratch/stefan/7769818/working/building/REAL300000237373 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237373 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237373/0 /scratch/stefan/7769818/working/building/REAL300000237373 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/373 `/scratch/stefan/7769818/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CSC(C(=O)[O-])=C2)C=C1) `REAL300000237373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237373 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CSC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 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, 6, 7, 7, 7, 7, 7, 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: [201, 201, 201, 152, 201, 75, 164, 164, 44, 6, 43, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 164, 164, 201, 201, 201, 201, 201, 201, 164, 164, 7, 6, 1, 1, 164, 164] 201 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 720 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237373 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CSC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 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, 6, 7, 7, 7, 7, 7, 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: [6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 91, 91, 164, 164, 164, 164, 164, 164, 164, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 91, 91, 164, 164, 1, 1] 201 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 35, 21, 22, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 341 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237373 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237373 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237373/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237373 Building REAL300000237374 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237374' /scratch/stefan/7769818/working/building/REAL300000237374 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237374 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237374/0 /scratch/stefan/7769818/working/building/REAL300000237374 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/374 `/scratch/stefan/7769818/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)=CC=C1OCC(=O)[O-]) `REAL300000237374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237374 none CCOC1=CC(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 18, 18, 18, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 18, 18, 18, 18, 77, 122, 126, 126, 35, 35, 35, 35, 35, 17, 6, 6, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 18, 18, 122, 122] 201 rigid atoms, others: [37, 38, 8, 10, 11, 12, 13, 14, 45, 19, 20, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50]) total number of confs: 442 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237374 none CCOC1=CC(C=CC(=O)C2=CC=C(C(=O)N(C)C)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 5, 5, 13, 13, 18, 18, 17, 18, 32, 32, 32, 32, 18, 18, 1, 1, 1, 1, 7, 18, 20, 20, 5, 5, 5, 5, 5, 1, 5, 5, 18, 18, 32, 32, 32, 32, 32, 32, 18, 18, 1, 1, 18, 18] 201 rigid atoms, others: [34, 3, 4, 5, 6, 2, 47, 48, 21, 22, 23, 24] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237374 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237374 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237374/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237374 Building REAL300000237375 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237375' /scratch/stefan/7769818/working/building/REAL300000237375 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237375 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237375/0 /scratch/stefan/7769818/working/building/REAL300000237375 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/375 `/scratch/stefan/7769818/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(F)=C(C(=O)[O-])C(F)=C2)C=C1) `REAL300000237375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237375 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(F)=C(C(=O)[O-])C(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 113, 178, 47, 129, 129, 31, 7, 30, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 129, 129, 178, 178, 178, 178, 178, 178, 129, 129, 7, 7, 1, 1, 129, 129] 178 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 629 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237375 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC(F)=C(C(=O)[O-])C(F)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 6, 10, 1, 6, 1, 1, 1, 1, 1, 12, 12, 96, 96, 140, 140, 140, 140, 140, 172, 172, 140, 140, 140, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1, 96, 96, 140, 140, 1, 1] 192 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 39, 24, 25, 38] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 455 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237375 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237375 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237375/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237375 Building REAL300000237376 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237376' /scratch/stefan/7769818/working/building/REAL300000237376 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237376 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237376/0 /scratch/stefan/7769818/working/building/REAL300000237376 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/376 `/scratch/stefan/7769818/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC3=C(C=C(C(=O)[O-])N3)O2)C=C1) `REAL300000237376.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237376 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC3=C(C=C(C(=O)[O-])N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 84, 93, 28, 84, 28, 68, 68, 28, 12, 28, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 68, 68, 93, 93, 93, 93, 93, 93, 68, 68, 12, 12, 1, 1, 1, 68, 68] 93 rigid atoms, others: [36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40]) total number of confs: 381 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237376 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC3=C(C=C(C(=O)[O-])N3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [7, 6, 7, 1, 6, 1, 1, 1, 1, 1, 12, 12, 41, 41, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 41, 41, 68, 68, 68, 1, 1] 93 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 39, 40, 24, 25] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237376 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237376 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237376/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237376 Building REAL300000237377 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237377' /scratch/stefan/7769818/working/building/REAL300000237377 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237377 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237377/0 /scratch/stefan/7769818/working/building/REAL300000237377 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/377 `/scratch/stefan/7769818/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)C=C1) `REAL300000237377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237377 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 167, 201, 119, 167, 167, 48, 5, 48, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 167, 167, 201, 201, 201, 201, 201, 201, 167, 167, 5, 5, 1, 1, 1, 1, 167, 167] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 627 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237377 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C3OC(C(=O)[O-])=CC3=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 10, 1, 6, 1, 1, 1, 1, 1, 12, 12, 88, 88, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1, 88, 88, 167, 167, 167, 167, 1, 1] 201 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 42, 41, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 360 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237377 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237377 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237377/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237377 Building REAL300000237378 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237378' /scratch/stefan/7769818/working/building/REAL300000237378 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237378 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237378/0 /scratch/stefan/7769818/working/building/REAL300000237378 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/378 `/scratch/stefan/7769818/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CN3C(C(=O)[O-])=CN=C23)C=C1) `REAL300000237378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237378 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CN3C(C(=O)[O-])=CN=C23)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 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, 6, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 186, 152, 186, 114, 152, 152, 61, 11, 61, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 152, 152, 186, 186, 186, 186, 186, 186, 152, 152, 11, 11, 1, 1, 1, 1, 152, 152] 186 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 575 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237378 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CN3C(C(=O)[O-])=CN=C23)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 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, 6, 7, 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, 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: [8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 54, 54, 152, 152, 152, 152, 152, 152, 152, 152, 152, 152, 152, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 54, 54, 152, 152, 152, 152, 1, 1] 186 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 42, 41, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 289 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237378 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237378 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237378/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237378 Building REAL300000237379 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237379' /scratch/stefan/7769818/working/building/REAL300000237379 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237379 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237379/0 /scratch/stefan/7769818/working/building/REAL300000237379 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/379 `/scratch/stefan/7769818/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CC=C(C(=O)N(C)C)C=C1) `REAL300000237379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237379 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CC=C(C(=O)N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 39, 39, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 10, 10, 1, 1, 94, 94, 94, 94, 94, 94, 94, 39, 39, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1] 156 rigid atoms, others: [38, 39, 46, 47, 16, 18, 19, 20, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 196 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237379 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CC=C(C(=O)N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 59, 60, 94, 94, 60, 74, 156, 156, 156, 156, 94, 94, 2, 2, 2, 1, 1, 1, 1, 10, 10, 94, 94, 156, 156, 156, 156, 156, 156, 94, 94] 156 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 34, 35] set([4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 607 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237379 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237379 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237379/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237379 Building REAL300000237380 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237380' /scratch/stefan/7769818/working/building/REAL300000237380 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237380 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237380/0 /scratch/stefan/7769818/working/building/REAL300000237380 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/380 `/scratch/stefan/7769818/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CN=C3C=CC(C(=O)[O-])=CN23)C=C1) `REAL300000237380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237380 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CN=C3C=CC(C(=O)[O-])=CN23)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', '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: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 182, 95, 182, 43, 141, 141, 43, 10, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 141, 141, 182, 182, 182, 182, 182, 182, 141, 141, 10, 10, 1, 1, 1, 1, 141, 141] 182 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 777 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237380 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CN=C3C=CC(C(=O)[O-])=CN23)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', '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: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 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, 6, 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, 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: [8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 51, 51, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 51, 51, 141, 141, 141, 141, 1, 1] 182 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 42, 41, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 268 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237380 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237380 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237380/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237380 Building REAL300000237381 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237381' /scratch/stefan/7769818/working/building/REAL300000237381 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237381 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237381/0 /scratch/stefan/7769818/working/building/REAL300000237381 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/381 `/scratch/stefan/7769818/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(N3C=NC(C(=O)[O-])=C3)C=C2)C=C1) `REAL300000237381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237381 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(N3C=NC(C(=O)[O-])=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.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, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 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, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 163, 56, 164, 54, 114, 114, 29, 4, 29, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 114, 114, 165, 165, 165, 161, 165, 165, 114, 114, 4, 4, 1, 1, 7, 7, 1, 1, 114, 114] 201 rigid atoms, others: [39, 40, 44, 43, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 45, 46]) total number of confs: 600 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237381 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(N3C=NC(C(=O)[O-])=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.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, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 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, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 145, 201, 144, 181, 181, 87, 15, 87, 15, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 181, 181, 201, 201, 201, 201, 201, 201, 181, 181, 15, 15, 7, 7, 1, 1, 7, 7, 181, 181] 201 rigid atoms, others: [41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46]) total number of confs: 652 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: REAL300000237381 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(N3C=NC(C(=O)[O-])=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.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, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 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, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 78, 78, 114, 114, 78, 78, 181, 181, 181, 181, 181, 181, 181, 114, 114, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 78, 78, 114, 114, 181, 181, 114, 114, 1, 1] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 45, 46, 3, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 519 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237381 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237381 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237381/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237381 Building REAL300000237382 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237382' /scratch/stefan/7769818/working/building/REAL300000237382 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237382 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237382/0 /scratch/stefan/7769818/working/building/REAL300000237382 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/382 `/scratch/stefan/7769818/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2F)C=C1) `REAL300000237382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237382 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 178, 201, 48, 178, 48, 131, 131, 48, 11, 48, 11, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 131, 131, 201, 201, 201, 201, 201, 201, 131, 131, 11, 11, 1, 1, 1, 131, 131] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 786 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237382 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=CC(C(=O)[O-])=C2F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 49, 49, 131, 131, 131, 131, 131, 165, 165, 131, 131, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 49, 49, 131, 131, 131, 1, 1] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 39, 23, 24, 38, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 385 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237382 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237382 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237382/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237382 Building REAL300000237383 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237383' /scratch/stefan/7769818/working/building/REAL300000237383 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237383 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237383/0 /scratch/stefan/7769818/working/building/REAL300000237383 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/383 `/scratch/stefan/7769818/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)C=C1) `REAL300000237383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237383 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 122, 122, 58, 122, 33, 58, 58, 13, 5, 13, 5, 1, 1, 1, 1, 1, 1, 5, 11, 20, 20, 1, 1, 1, 58, 58, 122, 122, 122, 122, 122, 122, 58, 58, 5, 5, 1, 1, 11, 11, 1, 58, 58] 201 rigid atoms, others: [37, 38, 41, 12, 13, 14, 15, 16, 17, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 42, 43]) total number of confs: 490 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237383 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 10, 19, 19, 58, 58, 34, 58, 144, 173, 183, 183, 58, 58, 58, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 19, 19, 58, 58, 173, 173, 58, 1, 1] 201 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 42, 43, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 577 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237383 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237383 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237383/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237383 Building REAL300000237384 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237384' /scratch/stefan/7769818/working/building/REAL300000237384 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237384 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237384/0 /scratch/stefan/7769818/working/building/REAL300000237384 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/384 `/scratch/stefan/7769818/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C3=CC=CC=C3C(=O)[O-])C=C2)C=C1) `REAL300000237384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237384 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C3=CC=CC=C3C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 116, 158, 21, 116, 21, 81, 81, 21, 3, 21, 3, 1, 1, 1, 1, 1, 1, 7, 7, 5, 7, 7, 7, 7, 7, 1, 1, 81, 81, 158, 158, 158, 158, 158, 158, 81, 81, 3, 3, 1, 1, 7, 7, 7, 7, 1, 1, 81, 81] 201 rigid atoms, others: [47, 40, 41, 12, 13, 14, 15, 16, 17, 46, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 48, 49]) total number of confs: 617 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237384 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C3=CC=CC=C3C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 201, 74, 195, 74, 174, 174, 74, 13, 74, 13, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 174, 174, 201, 201, 201, 201, 201, 201, 174, 174, 13, 13, 7, 7, 1, 1, 1, 1, 7, 7, 174, 174] 201 rigid atoms, others: [44, 42, 43, 45, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49]) total number of confs: 874 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: REAL300000237384 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=CC=C(C3=CC=CC=C3C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 59, 59, 81, 81, 59, 81, 174, 174, 151, 174, 174, 174, 174, 174, 81, 81, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 59, 59, 81, 81, 174, 174, 170, 174, 81, 81, 1, 1] 201 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 48, 49, 28, 29, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 543 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237384 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237384 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237384/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237384 Building REAL300000237385 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237385' /scratch/stefan/7769818/working/building/REAL300000237385 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237385 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237385/0 /scratch/stefan/7769818/working/building/REAL300000237385 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/385 `/scratch/stefan/7769818/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC=C(C(=O)N(C)C)C=C1) `REAL300000237385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237385 none COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC=C(C(=O)N(C)C)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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 143, 143, 143, 143, 143, 143, 143, 143, 143, 48, 48, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 11, 11, 1, 1, 157, 157, 157, 143, 143, 143, 48, 48, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1] 201 rigid atoms, others: [34, 35, 42, 43, 13, 15, 16, 17, 18, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 297 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237385 none COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC=C(C(=O)N(C)C)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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 79, 79, 143, 143, 95, 143, 201, 201, 201, 201, 143, 143, 4, 4, 4, 1, 1, 1, 9, 9, 143, 143, 201, 201, 201, 201, 201, 201, 143, 143] 201 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, 42, 43]) total number of confs: 701 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237385 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237385 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237385/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237385 Building REAL300000237386 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237386' /scratch/stefan/7769818/working/building/REAL300000237386 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237386 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237386/0 /scratch/stefan/7769818/working/building/REAL300000237386 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/386 `/scratch/stefan/7769818/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=C(C(=O)C=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)C=C1) `REAL300000237386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237386 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 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, 6, 7, 7, 7, 7, 7, 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 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 69, 163, 41, 125, 125, 41, 9, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 125, 125, 163, 163, 163, 163, 163, 163, 125, 125, 9, 9, 1, 1, 1, 125, 125] 163 rigid atoms, others: [38, 39, 40, 12, 13, 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, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42]) total number of confs: 662 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237386 none CN(C)C(=O)C1=CC=C(C(=O)C=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 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, 6, 7, 7, 7, 7, 7, 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 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 12, 12, 51, 51, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 51, 51, 125, 125, 125, 1, 1] 163 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 42, 35, 41, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 249 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237386 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237386 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237386/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237386 Building REAL300000237387 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237387' /scratch/stefan/7769818/working/building/REAL300000237387 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237387 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237387/0 /scratch/stefan/7769818/working/building/REAL300000237387 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/387 `/scratch/stefan/7769818/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)=CC=C1OCC(=O)[O-]) `REAL300000237387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237387 none COC1=CC(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 81, 197, 201, 201, 31, 31, 31, 11, 1, 2, 2, 2, 1, 1, 11, 11, 197, 197] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 660 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237387 none COC1=CC(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 9, 52, 81, 81, 4, 4, 4, 1, 11, 11, 11, 11, 11, 11, 1, 1, 52, 52] 201 rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 20, 21, 36, 29, 37] set([0, 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, 38, 39]) total number of confs: 292 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237387 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237387 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237387/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237387 Building REAL300000237388 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237388' /scratch/stefan/7769818/working/building/REAL300000237388 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237388 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237388/0 /scratch/stefan/7769818/working/building/REAL300000237388 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/388 `/scratch/stefan/7769818/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])C=C1)C2=O) `REAL300000237388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237388 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1] 3 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 7 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237388 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 3, 1, 1, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 25, 26, 27] set([12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237388 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237388 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237388/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237388 Building REAL300000237389 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237389' /scratch/stefan/7769818/working/building/REAL300000237389 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237389 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237389/0 /scratch/stefan/7769818/working/building/REAL300000237389 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/389 `/scratch/stefan/7769818/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(OCC(=O)[O-])C=C1)C2=O) `REAL300000237389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237389 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(OCC(=O)[O-])C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 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] 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: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 22, 28, 28, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 22, 22, 1, 1] 42 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 105 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237389 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(OCC(=O)[O-])C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 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] 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, 1, 1, 1, 1, 1, 1, 6, 6, 3, 6, 19, 42, 42, 42, 6, 6, 1, 1, 2, 2, 2, 1, 1, 1, 6, 6, 42, 42, 6, 6] 42 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 27, 28, 29] set([32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 30, 31]) total number of confs: 145 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237389 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237389 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237389/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237389 Building REAL300000237390 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237390' /scratch/stefan/7769818/working/building/REAL300000237390 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237390 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237390/0 /scratch/stefan/7769818/working/building/REAL300000237390 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/390 `/scratch/stefan/7769818/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(OCCC(=O)[O-])C=C1)C2=O) `REAL300000237390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237390 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(OCCC(=O)[O-])C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.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, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 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, 7, 3, 7, 7, 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] 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: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 26, 39, 51, 46, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 26, 26, 39, 39, 1, 1] 79 rigid atoms, others: [32, 37, 38, 10, 11, 12, 13, 14, 15, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 200 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237390 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(OCCC(=O)[O-])C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.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, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 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, 7, 3, 7, 7, 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] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 3, 6, 26, 61, 79, 79, 79, 6, 6, 1, 1, 2, 2, 2, 1, 1, 1, 6, 6, 61, 61, 79, 79, 6, 6] 79 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 28, 29, 30] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 293 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237390 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237390 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237390/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237390 Building REAL300000237391 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237391' /scratch/stefan/7769818/working/building/REAL300000237391 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237391 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237391/0 /scratch/stefan/7769818/working/building/REAL300000237391 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/391 `/scratch/stefan/7769818/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(OC(C)C(=O)[O-])=C1)C2=O) `REAL300000237391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237391 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(OC(C)C(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.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, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 13, 40, 40, 52, 52, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 40, 40, 40, 40, 1] 145 rigid atoms, others: [32, 33, 38, 10, 11, 12, 13, 14, 15, 16, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 201 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237391 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(OC(C)C(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.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, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 90, 145, 145, 145, 145, 11, 1, 1, 2, 2, 2, 1, 1, 1, 11, 11, 11, 145, 145, 145, 145, 11] 145 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 28, 29, 30] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 422 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237391 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237391 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237391/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237391 Building REAL300000237392 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237392' /scratch/stefan/7769818/working/building/REAL300000237392 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237392 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237392/0 /scratch/stefan/7769818/working/building/REAL300000237392 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/392 `/scratch/stefan/7769818/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(OCCC(=O)[O-])=C1)C2=O) `REAL300000237392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237392 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(OCCC(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.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, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 6, 25, 35, 53, 42, 1, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 25, 25, 35, 35, 1] 159 rigid atoms, others: [32, 33, 38, 10, 11, 12, 13, 14, 15, 16, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 217 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237392 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(OCCC(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.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, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 11, 12, 12, 48, 110, 159, 159, 152, 12, 1, 1, 2, 2, 2, 1, 1, 1, 12, 12, 12, 110, 110, 159, 159, 12] 159 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 28, 29, 30] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 608 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237392 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237392 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237392/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237392 Building REAL300000237393 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237393' /scratch/stefan/7769818/working/building/REAL300000237393 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237393 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237393/0 /scratch/stefan/7769818/working/building/REAL300000237393 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/393 `/scratch/stefan/7769818/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(C(=O)[O-])C=C3)O1)C2=O) `REAL300000237393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237393 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(C(=O)[O-])C=C3)O1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 12, 12, 13, 13, 13, 13, 13, 12, 1, 1, 6, 6, 6, 6] 28 rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237393 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(C(=O)[O-])C=C3)O1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 3, 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, 28, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 6, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 1, 1, 1, 1] 28 rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 61 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: REAL300000237393 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(C(=O)[O-])C=C3)O1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 12, 1, 1, 2, 2, 2, 1, 1, 1, 12, 12, 28, 28, 28, 28] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 25, 26, 30, 31] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 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 /scratch/stefan/7769818/working/building/REAL300000237393 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237393 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237393/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237393 Building REAL300000237394 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237394' /scratch/stefan/7769818/working/building/REAL300000237394 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237394 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237394/0 /scratch/stefan/7769818/working/building/REAL300000237394 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/394 `/scratch/stefan/7769818/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(OCC(=O)[O-])=C1)C2=O) `REAL300000237394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237394 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(OCC(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 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: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 25, 45, 45, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 25, 25, 1] 118 rigid atoms, others: [32, 35, 10, 11, 12, 13, 14, 15, 16, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 172 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237394 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(OCC(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 41, 118, 118, 118, 11, 1, 1, 2, 2, 2, 1, 1, 1, 11, 11, 11, 118, 118, 11] 118 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 27, 28, 29] set([32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 30, 31]) total number of confs: 400 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237394 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237394 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237394/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237394 Building REAL300000237395 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237395' /scratch/stefan/7769818/working/building/REAL300000237395 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237395 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237395/0 /scratch/stefan/7769818/working/building/REAL300000237395 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/395 `/scratch/stefan/7769818/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(OC(F)(F)C(=O)[O-])C=C1)C2=O) `REAL300000237395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237395 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(OC(F)(F)C(=O)[O-])C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 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: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 64, 64, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 94 rigid atoms, others: [32, 33, 34, 35, 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]) total number of confs: 219 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237395 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(OC(F)(F)C(=O)[O-])C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 3, 6, 40, 94, 94, 94, 94, 94, 6, 6, 1, 1, 2, 2, 2, 1, 1, 1, 6, 6, 6, 6] 94 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 29, 30, 31] set([32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237395 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237395 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237395/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237395 Building REAL300000237396 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237396' /scratch/stefan/7769818/working/building/REAL300000237396 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237396 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237396/0 /scratch/stefan/7769818/working/building/REAL300000237396 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/396 `/scratch/stefan/7769818/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)C=C1) `REAL300000237396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237396 none COC1=C2OC(C(=O)[O-])=CC2=C(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 1, 1, 9, 9] 9 rigid atoms, others: [35, 36, 11, 12, 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, 25, 26, 27, 28, 29, 30, 32, 33, 34, 37, 38]) total number of confs: 16 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237396 none COC1=C2OC(C(=O)[O-])=CC2=C(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 3, 3, 3, 1, 9, 9, 9, 9, 9, 9, 1, 1] 9 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 25, 26, 38, 30, 37] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237396 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237396 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237396/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237396 Building REAL300000237397 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237397' /scratch/stefan/7769818/working/building/REAL300000237397 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237397 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237397/0 /scratch/stefan/7769818/working/building/REAL300000237397 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/397 `/scratch/stefan/7769818/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CN(CC(=O)[O-])N=N1)C2=O) `REAL300000237397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237397 none CC1=CC(Cl)=CC2=C1OC(=CC1=CN(CC(=O)[O-])N=N1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 1, 1, 1, 1, 1, 7, 10, 10, 1, 1, 9, 9, 10, 10, 10, 10, 10, 9, 1, 7, 7] 26 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 54 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237397 none CC1=CC(Cl)=CC2=C1OC(=CC1=CN(CC(=O)[O-])N=N1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 26, 26, 9, 9, 1, 1, 2, 2, 2, 1, 1, 1, 9, 26, 26] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 25, 26, 27] set([12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 28, 29, 30]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237397 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237397 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237397/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237397 Building REAL300000237398 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237398' /scratch/stefan/7769818/working/building/REAL300000237398 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237398 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237398/0 /scratch/stefan/7769818/working/building/REAL300000237398 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/398 `/scratch/stefan/7769818/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(C(=O)[O-])=C1)C2=O) `REAL300000237398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237398 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(C(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 5 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237398 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(C(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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 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, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 25, 26, 27] set([12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 12 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237398 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237398 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237398/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237398 Building REAL300000237399 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237399' /scratch/stefan/7769818/working/building/REAL300000237399 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237399 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237399/0 /scratch/stefan/7769818/working/building/REAL300000237399 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/399 `/scratch/stefan/7769818/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC(C(=O)[O-])=CS1)C2=O) `REAL300000237399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237399 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC(C(=O)[O-])=CS1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237399 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC(C(=O)[O-])=CS1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 2, 2, 2, 1, 1, 1, 7, 7] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26] set([12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 27, 28]) total number of confs: 14 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237399 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237399 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237399/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237399 Building REAL300000237400 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237400' /scratch/stefan/7769818/working/building/REAL300000237400 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237400 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237400/0 /scratch/stefan/7769818/working/building/REAL300000237400 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/400 `/scratch/stefan/7769818/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)=CC=C1OCCC(=O)[O-]) `REAL300000237400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237400 none COC1=CC(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 70, 150, 201, 201, 201, 28, 28, 28, 11, 1, 2, 2, 2, 1, 1, 11, 11, 150, 150, 201, 201] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 36, 31] set([0, 1, 2, 3, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 749 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237400 none COC1=CC(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 9, 38, 70, 91, 91, 4, 4, 4, 1, 11, 11, 11, 11, 11, 11, 1, 1, 38, 38, 70, 70] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 18, 19, 20, 21, 30, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 390 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237400 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237400 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237400/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237400 Building REAL300000237401 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237401' /scratch/stefan/7769818/working/building/REAL300000237401 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237401 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237401/0 /scratch/stefan/7769818/working/building/REAL300000237401 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/401 `/scratch/stefan/7769818/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])C=C1Cl)C2=O) `REAL300000237401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237401 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])C=C1Cl)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1] 5 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237401 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])C=C1Cl)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 2, 1, 1, 1, 5, 5, 5] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 26, 27, 28] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31]) total number of confs: 12 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237401 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237401 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237401/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237401 Building REAL300000237402 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237402' /scratch/stefan/7769818/working/building/REAL300000237402 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237402 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237402/0 /scratch/stefan/7769818/working/building/REAL300000237402 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/402 `/scratch/stefan/7769818/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(C(=O)[O-])=C1Cl)C2=O) `REAL300000237402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237402 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(C(=O)[O-])=C1Cl)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1] 9 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237402 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(C(=O)[O-])=C1Cl)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 2, 2, 2, 1, 1, 1, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 26, 27, 28] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237402 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237402 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237402/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237402 Building REAL300000237403 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237403' /scratch/stefan/7769818/working/building/REAL300000237403 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237403 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237403/0 /scratch/stefan/7769818/working/building/REAL300000237403 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/403 `/scratch/stefan/7769818/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(O)C(C(=O)[O-])=C1)C2=O) `REAL300000237403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237403 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(O)C(C(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 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, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 1] 10 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237403 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(O)C(C(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 2, 1, 1, 1, 5, 5, 10, 5] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 26, 27, 28] set([32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237403 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237403 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237403/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237403 Building REAL300000237404 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237404' /scratch/stefan/7769818/working/building/REAL300000237404 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237404 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237404/0 /scratch/stefan/7769818/working/building/REAL300000237404 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/404 `/scratch/stefan/7769818/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=C1OC2=C(C)C=C(Cl)C=C2C1=O) `REAL300000237404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237404 none CC1=CC(C)=C(C(=O)[O-])C=C1C=C1OC2=C(C)C=C(Cl)C=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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, 5, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2, 1, 1] 5 rigid atoms, others: [32, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 33, 35, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 12 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237404 none CC1=CC(C)=C(C(=O)[O-])C=C1C=C1OC2=C(C)C=C(Cl)C=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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, 5, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 2, 2, 2, 1, 5, 5, 5, 5, 5, 5] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 27, 31] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237404 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237404 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237404/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237404 Building REAL300000237405 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237405' /scratch/stefan/7769818/working/building/REAL300000237405 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237405 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237405/0 /scratch/stefan/7769818/working/building/REAL300000237405 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/405 `/scratch/stefan/7769818/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(OC(C)C(=O)[O-])C=C1)C2=O) `REAL300000237405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237405 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(OC(C)C(=O)[O-])C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.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, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 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, 7, 3, 7, 7, 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] 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: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 13, 34, 34, 41, 41, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 34, 34, 34, 34, 1, 1] 55 rigid atoms, others: [32, 37, 38, 10, 11, 12, 13, 14, 15, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 150 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237405 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(OC(C)C(=O)[O-])C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.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, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 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, 7, 3, 7, 7, 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] 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, 1, 6, 6, 3, 6, 40, 55, 55, 55, 55, 6, 6, 1, 1, 2, 2, 2, 1, 1, 1, 6, 6, 55, 55, 55, 55, 6, 6] 55 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 28, 29, 30] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 148 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237405 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237405 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237405/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237405 Building REAL300000237406 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237406' /scratch/stefan/7769818/working/building/REAL300000237406 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237406 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237406/0 /scratch/stefan/7769818/working/building/REAL300000237406 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/406 `/scratch/stefan/7769818/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])C(F)=C1)C2=O) `REAL300000237406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237406 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])C(F)=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1] 5 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237406 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])C(F)=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 2, 1, 1, 1, 5, 5, 5] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 26, 27, 28] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31]) total number of confs: 12 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237406 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237406 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237406/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237406 Building REAL300000237407 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237407' /scratch/stefan/7769818/working/building/REAL300000237407 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237407 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237407/0 /scratch/stefan/7769818/working/building/REAL300000237407 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/407 `/scratch/stefan/7769818/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C=CC(=O)[O-])O1)C2=O) `REAL300000237407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237407 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C=CC(=O)[O-])O1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 1, 12, 12, 13, 13, 13, 13, 13, 12, 1, 1, 7, 7] 28 rigid atoms, others: [10, 11, 12, 13, 14, 15, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237407 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C=CC(=O)[O-])O1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 28, 28, 28, 28, 12, 1, 1, 2, 2, 2, 1, 1, 1, 13, 12, 27, 28] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 26, 27, 28] set([32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237407 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237407 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237407/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237407 Building REAL300000237408 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237408' /scratch/stefan/7769818/working/building/REAL300000237408 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237408 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237408/0 /scratch/stefan/7769818/working/building/REAL300000237408 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/408 `/scratch/stefan/7769818/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)C=C1C(=O)[O-]) `REAL300000237408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237408 none COC1=CC=C(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 21, 21, 21, 21, 21, 11, 11, 1, 2, 2, 2, 1, 1, 11] 21 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 35, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237408 none COC1=CC=C(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 11, 11, 11, 11, 11, 11, 1] 21 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 27, 28, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237408 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237408 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237408/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237408 Building REAL300000237409 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237409' /scratch/stefan/7769818/working/building/REAL300000237409 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237409 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237409/0 /scratch/stefan/7769818/working/building/REAL300000237409 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/409 `/scratch/stefan/7769818/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC(C(=O)[O-])=CC=C1F)C2=O) `REAL300000237409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237409 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC(C(=O)[O-])=CC=C1F)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1] 7 rigid atoms, others: [10, 11, 12, 13, 14, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237409 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC(C(=O)[O-])=CC=C1F)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 2, 2, 2, 1, 1, 1, 7, 7, 7] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 26, 27, 28] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31]) total number of confs: 14 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237409 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237409 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237409/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237409 Building REAL300000237410 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237410' /scratch/stefan/7769818/working/building/REAL300000237410 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237410 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237410/0 /scratch/stefan/7769818/working/building/REAL300000237410 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/410 `/scratch/stefan/7769818/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(F)C(C(=O)[O-])=C1)C2=O) `REAL300000237410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237410 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(F)C(C(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1] 11 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237410 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(F)C(C(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 2, 2, 2, 1, 1, 1, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 26, 27, 28] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31]) total number of confs: 18 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237410 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237410 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237410/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237410 Building REAL300000237411 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237411' /scratch/stefan/7769818/working/building/REAL300000237411 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237411 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237411/0 /scratch/stefan/7769818/working/building/REAL300000237411 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/411 `/scratch/stefan/7769818/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(CC(=O)[O-])C=C1)C2=O) `REAL300000237411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237411 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(CC(=O)[O-])C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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] 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, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 2, 2, 1, 1] 5 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: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237411 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(CC(=O)[O-])C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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] 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, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 3, 3, 1, 1, 2, 2, 2, 1, 1, 1, 3, 3, 5, 5, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 26, 27, 28] set([32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237411 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237411 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237411/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237411 Building REAL300000237412 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237412' /scratch/stefan/7769818/working/building/REAL300000237412 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237412 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237412/0 /scratch/stefan/7769818/working/building/REAL300000237412 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/412 `/scratch/stefan/7769818/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC(Br)=CC(C(=O)[O-])=C1)C2=O) `REAL300000237412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237412 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC(Br)=CC(C(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1] 11 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237412 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC(Br)=CC(C(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 2, 2, 2, 1, 1, 1, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 26, 27, 28] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31]) total number of confs: 18 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237412 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237412 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237412/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237412 Building REAL300000237413 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237413' /scratch/stefan/7769818/working/building/REAL300000237413 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237413 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237413/0 /scratch/stefan/7769818/working/building/REAL300000237413 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/413 `/scratch/stefan/7769818/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])S1)C2=O) `REAL300000237413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237413 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])S1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237413 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])S1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 2, 2, 2, 1, 1, 1, 7, 7] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26] set([12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 27, 28]) total number of confs: 14 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237413 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237413 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237413/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237413 Building REAL300000237414 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237414' /scratch/stefan/7769818/working/building/REAL300000237414 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237414 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237414/0 /scratch/stefan/7769818/working/building/REAL300000237414 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/414 `/scratch/stefan/7769818/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C=CC(=O)[O-])C=C1)C2=O) `REAL300000237414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237414 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C=CC(=O)[O-])C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 5, 5, 1, 1] 7 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 25 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237414 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C=CC(=O)[O-])C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 5, 5, 1, 1, 2, 2, 2, 1, 1, 1, 5, 5, 7, 7, 5, 5] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 27, 28, 29] set([32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 30, 31]) total number of confs: 32 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237414 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237414 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237414/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237414 Building REAL300000237415 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237415' /scratch/stefan/7769818/working/building/REAL300000237415 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237415 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237415/0 /scratch/stefan/7769818/working/building/REAL300000237415 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/415 `/scratch/stefan/7769818/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC(F)=C(C(=O)[O-])C=C1F)C2=O) `REAL300000237415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237415 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC(F)=C(C(=O)[O-])C=C1F)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1] 10 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237415 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC(F)=C(C(=O)[O-])C=C1F)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 9, 9, 10, 10, 10, 10, 10, 1, 1, 2, 2, 2, 1, 1, 1, 10, 10] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 27, 28, 29] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 30, 31]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237415 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237415 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237415/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237415 Building REAL300000237416 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237416' /scratch/stefan/7769818/working/building/REAL300000237416 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237416 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237416/0 /scratch/stefan/7769818/working/building/REAL300000237416 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/416 `/scratch/stefan/7769818/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=C3C(=CC=C1)NN=C3C(=O)[O-])C2=O) `REAL300000237416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237416 none CC1=CC(Cl)=CC2=C1OC(=CC1=C3C(=CC=C1)NN=C3C(=O)[O-])C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 7 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237416 none CC1=CC(Cl)=CC2=C1OC(=CC1=C3C(=CC=C1)NN=C3C(=O)[O-])C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 2, 2, 2, 1, 1, 1, 7, 7, 7, 7] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 28, 29, 30] set([32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 31]) total number of confs: 14 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237416 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237416 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237416/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237416 Building REAL300000237417 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237417' /scratch/stefan/7769818/working/building/REAL300000237417 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237417 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237417/0 /scratch/stefan/7769818/working/building/REAL300000237417 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/417 `/scratch/stefan/7769818/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(C(=O)[O-])C(O)=C3)O1)C2=O) `REAL300000237417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237417 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(C(=O)[O-])C(O)=C3)O1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 20, 20, 12, 12, 12, 1, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 12, 12, 24, 12] 136 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237417 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(C(=O)[O-])C(O)=C3)O1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 12, 68, 68, 68, 68, 68, 68, 68, 68, 12, 12, 1, 1, 2, 1] 136 rigid atoms, others: [36, 37, 39, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 149 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: REAL300000237417 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(C(=O)[O-])C(O)=C3)O1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 68, 68, 68, 68, 68, 68, 68, 68, 68, 13, 1, 1, 2, 2, 2, 1, 1, 1, 13, 13, 68, 68, 136, 68] 136 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 32, 26, 27, 31] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237417 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237417 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237417/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237417 Building REAL300000237418 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237418' /scratch/stefan/7769818/working/building/REAL300000237418 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237418 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237418/0 /scratch/stefan/7769818/working/building/REAL300000237418 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/418 `/scratch/stefan/7769818/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C1)C2=O) `REAL300000237418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237418 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', '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', 'C.ar', 'C.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, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3, 3, 3, 1, 1] 4 rigid atoms, others: [34, 35, 40, 41, 10, 11, 12, 13, 14, 15, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 15 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237418 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', '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', 'C.ar', 'C.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, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 1, 1, 1, 1, 3, 3] 4 rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 16 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: REAL300000237418 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(C(=O)[O-])C=C3)C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', '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', 'C.ar', 'C.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, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 3, 4, 4, 4, 4, 4, 3, 3, 1, 1, 2, 2, 2, 1, 1, 1, 3, 3, 4, 4, 4, 4, 3, 3] 4 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 32, 26, 27, 31] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 17 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237418 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237418 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237418/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237418 Building REAL300000237419 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237419' /scratch/stefan/7769818/working/building/REAL300000237419 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237419 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237419/0 /scratch/stefan/7769818/working/building/REAL300000237419 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/419 `/scratch/stefan/7769818/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CNC3=CC=C(C(=O)[O-])C=C13)C2=O) `REAL300000237419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237419 none CC1=CC(Cl)=CC2=C1OC(=CC1=CNC3=CC=C(C(=O)[O-])C=C13)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1] 10 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237419 none CC1=CC(Cl)=CC2=C1OC(=CC1=CNC3=CC=C(C(=O)[O-])C=C13)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 2, 2, 2, 1, 1, 1, 10, 10, 10, 10, 10] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 28, 29, 30] set([32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 31]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237419 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237419 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237419/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237419 Building REAL300000237420 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237420' /scratch/stefan/7769818/working/building/REAL300000237420 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237420 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237420/0 /scratch/stefan/7769818/working/building/REAL300000237420 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/420 `/scratch/stefan/7769818/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])N=C1)C2=O) `REAL300000237420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237420 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])N=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1] 5 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237420 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])N=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 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, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 2, 1, 1, 1, 5, 5, 5] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 25, 26, 27] set([12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 28, 29, 30]) total number of confs: 12 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237420 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237420 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237420/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237420 Building REAL300000237421 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237421' /scratch/stefan/7769818/working/building/REAL300000237421 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237421 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237421/0 /scratch/stefan/7769818/working/building/REAL300000237421 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/421 `/scratch/stefan/7769818/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])C(O)=C1)C2=O) `REAL300000237421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237421 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])C(O)=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 1] 10 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237421 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])C(O)=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 2, 1, 1, 1, 5, 5, 10, 5] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 26, 27, 28] set([32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237421 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237421 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237421/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237421 Building REAL300000237422 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237422' /scratch/stefan/7769818/working/building/REAL300000237422 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237422 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237422/0 /scratch/stefan/7769818/working/building/REAL300000237422 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/422 `/scratch/stefan/7769818/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)C=C1C(=O)[O-]) `REAL300000237422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237422 none CC1=CC=C(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 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, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 1, 1, 11] 11 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 34, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 18 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237422 none CC1=CC=C(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 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, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 11, 11, 11, 11, 11, 11, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 18, 19, 20, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237422 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237422 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237422/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237422 Building REAL300000237423 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237423' /scratch/stefan/7769818/working/building/REAL300000237423 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237423 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237423/0 /scratch/stefan/7769818/working/building/REAL300000237423 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/423 `/scratch/stefan/7769818/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC(C(=O)[O-])=C(Cl)S1)C2=O) `REAL300000237423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237423 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC(C(=O)[O-])=C(Cl)S1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 11, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 12, 12, 13, 13, 13, 13, 13, 12, 1] 13 rigid atoms, others: [10, 11, 12, 13, 14, 17, 18, 19, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237423 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC(C(=O)[O-])=C(Cl)S1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 11, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 13, 13, 12, 12, 12, 1, 1, 2, 2, 2, 1, 1, 1, 12] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 25, 26, 27] set([12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 28]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237423 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237423 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237423/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237423 Building REAL300000237424 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237424' /scratch/stefan/7769818/working/building/REAL300000237424 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237424 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237424/0 /scratch/stefan/7769818/working/building/REAL300000237424 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/424 `/scratch/stefan/7769818/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=C2OC3=C(C=C(Cl)C=C3C)C2=O)O1) `REAL300000237424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237424 none CC1=C(C(=O)[O-])C=C(C=C2OC3=C(C=C(Cl)C=C3C)C2=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 10, 10, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 9, 1, 1, 1, 2, 2, 2] 10 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 26 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237424 none CC1=C(C(=O)[O-])C=C(C=C2OC3=C(C=C(Cl)C=C3C)C2=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 1, 9, 9, 9, 10, 10, 10] 10 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 21, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237424 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237424 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237424/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237424 Building REAL300000237425 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237425' /scratch/stefan/7769818/working/building/REAL300000237425 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237425 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237425/0 /scratch/stefan/7769818/working/building/REAL300000237425 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/425 `/scratch/stefan/7769818/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(C(=O)[O-])C=C3)S1)C2=O) `REAL300000237425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237425 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(C(=O)[O-])C=C3)S1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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] 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, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 6, 6, 1, 2, 6, 6, 6, 6, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 6, 6, 6, 6] 15 rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237425 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(C(=O)[O-])C=C3)S1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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] 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, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 6, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 1, 1, 1, 1] 15 rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 39 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: REAL300000237425 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(C(=O)[O-])C=C3)S1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 15, 15, 11, 15, 15, 15, 15, 15, 11, 1, 1, 2, 2, 2, 1, 1, 1, 11, 11, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 25, 26, 30, 31] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237425 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237425 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237425/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237425 Building REAL300000237426 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237426' /scratch/stefan/7769818/working/building/REAL300000237426 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237426 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237426/0 /scratch/stefan/7769818/working/building/REAL300000237426 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/426 `/scratch/stefan/7769818/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC(C(=O)[O-])=NN1C)C2=O) `REAL300000237426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237426 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC(C(=O)[O-])=NN1C)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2] 5 rigid atoms, others: [10, 11, 12, 13, 14, 17, 18, 19, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237426 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC(C(=O)[O-])=NN1C)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 25, 26, 27] set([12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 12 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237426 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237426 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237426/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237426 Building REAL300000237427 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237427' /scratch/stefan/7769818/working/building/REAL300000237427 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237427 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237427/0 /scratch/stefan/7769818/working/building/REAL300000237427 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/427 `/scratch/stefan/7769818/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O1)C2=O) `REAL300000237427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237427 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 13, 13, 12, 1, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 12, 12, 24, 12] 102 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237427 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 51, 50, 51, 51, 51, 51, 51, 51, 12, 12, 1, 1, 2, 1] 102 rigid atoms, others: [36, 37, 39, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 120 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: REAL300000237427 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 51, 51, 51, 51, 51, 51, 51, 51, 51, 13, 1, 1, 2, 2, 2, 1, 1, 1, 13, 13, 50, 51, 102, 51] 102 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 32, 26, 27, 31] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237427 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237427 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237427/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237427 Building REAL300000237428 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237428' /scratch/stefan/7769818/working/building/REAL300000237428 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237428 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237428/0 /scratch/stefan/7769818/working/building/REAL300000237428 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/428 `/scratch/stefan/7769818/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CN=CC(C(=O)[O-])=C1)C2=O) `REAL300000237428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237428 none CC1=CC(Cl)=CC2=C1OC(=CC1=CN=CC(C(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1] 6 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237428 none CC1=CC(Cl)=CC2=C1OC(=CC1=CN=CC(C(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 2, 2, 2, 1, 1, 1, 6, 6, 6] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 25, 26, 27] set([12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 28, 29, 30]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237428 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237428 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237428/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237428 Building REAL300000237429 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237429' /scratch/stefan/7769818/working/building/REAL300000237429 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237429 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237429/0 /scratch/stefan/7769818/working/building/REAL300000237429 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/429 `/scratch/stefan/7769818/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC(C(=O)[O-])=CO1)C2=O) `REAL300000237429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237429 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC(C(=O)[O-])=CO1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 5, 1, 1] 6 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237429 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC(C(=O)[O-])=CO1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 5, 5, 5, 1, 1, 2, 2, 2, 1, 1, 1, 6, 5] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26] set([12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 27, 28]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237429 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237429 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237429/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237429 Building REAL300000237430 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237430' /scratch/stefan/7769818/working/building/REAL300000237430 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237430 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237430/0 /scratch/stefan/7769818/working/building/REAL300000237430 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/430 `/scratch/stefan/7769818/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=CC(C(=O)[O-])=C3)S1)C2=O) `REAL300000237430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237430 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=CC(C(=O)[O-])=C3)S1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 12, 1, 12, 12, 13, 13, 13, 13, 13, 12, 1, 1, 12, 12, 12, 12] 37 rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237430 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=CC(C(=O)[O-])=C3)S1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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] 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, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 37, 37, 37, 37, 37, 37, 37, 37, 12, 12, 1, 1, 1, 1] 37 rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 83 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: REAL300000237430 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=CC(C(=O)[O-])=C3)S1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 37, 37, 37, 37, 37, 37, 37, 37, 12, 1, 1, 2, 2, 2, 1, 1, 1, 13, 12, 37, 37, 37, 37] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 25, 26, 30, 31] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237430 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237430 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237430/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237430 Building REAL300000237431 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237431' /scratch/stefan/7769818/working/building/REAL300000237431 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237431 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237431/0 /scratch/stefan/7769818/working/building/REAL300000237431 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/431 `/scratch/stefan/7769818/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=C1OC2=C(C)C=C(Cl)C=C2C1=O) `REAL300000237431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237431 none COC1=CC=C(C(=O)[O-])C=C1C=C1OC2=C(C)C=C(Cl)C=C2C1=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', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 11, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 1, 1] 9 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 32, 24, 25, 26, 27, 28, 29, 31]) total number of confs: 16 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237431 none COC1=CC=C(C(=O)[O-])C=C1C=C1OC2=C(C)C=C(Cl)C=C2C1=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', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 11, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 1, 1, 1, 9, 9, 9, 9, 9, 9] 9 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 27, 28, 29] set([0, 7, 8, 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: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237431 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237431 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237431/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237431 Building REAL300000237432 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237432' /scratch/stefan/7769818/working/building/REAL300000237432 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237432 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237432/0 /scratch/stefan/7769818/working/building/REAL300000237432 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/432 `/scratch/stefan/7769818/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CSC3=CC=C(C(=O)[O-])C=C13)C2=O) `REAL300000237432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237432 none CC1=CC(Cl)=CC2=C1OC(=CC1=CSC3=CC=C(C(=O)[O-])C=C13)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1] 10 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237432 none CC1=CC(Cl)=CC2=C1OC(=CC1=CSC3=CC=C(C(=O)[O-])C=C13)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 2, 2, 2, 1, 1, 1, 10, 10, 10, 10] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 28, 29, 30] set([32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 31]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237432 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237432 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237432/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237432 Building REAL300000237433 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237433' /scratch/stefan/7769818/working/building/REAL300000237433 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237433 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237433/0 /scratch/stefan/7769818/working/building/REAL300000237433 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/433 `/scratch/stefan/7769818/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC(C(=O)[O-])=CC=C1Br)C2=O) `REAL300000237433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237433 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC(C(=O)[O-])=CC=C1Br)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1] 7 rigid atoms, others: [10, 11, 12, 13, 14, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237433 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC(C(=O)[O-])=CC=C1Br)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 2, 2, 2, 1, 1, 1, 7, 7, 7] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 26, 27, 28] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31]) total number of confs: 14 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237433 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237433 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237433/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237433 Building REAL300000237434 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237434' /scratch/stefan/7769818/working/building/REAL300000237434 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237434 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237434/0 /scratch/stefan/7769818/working/building/REAL300000237434 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/434 `/scratch/stefan/7769818/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])C=C1[N+](=O)[O-])C2=O) `REAL300000237434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237434 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])C=C1[N+](=O)[O-])C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1] 5 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237434 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C(=O)[O-])C=C1[N+](=O)[O-])C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 3, 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, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 2, 1, 1, 1, 5, 5, 5] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 28, 29, 30] set([32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 31]) total number of confs: 12 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237434 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237434 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237434/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237434 Building REAL300000237435 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237435' /scratch/stefan/7769818/working/building/REAL300000237435 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237435 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237435/0 /scratch/stefan/7769818/working/building/REAL300000237435 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/435 `/scratch/stefan/7769818/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(CC(=O)[O-])=C1)C2=O) `REAL300000237435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237435 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(CC(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 1] 21 rigid atoms, others: [34, 10, 11, 12, 13, 14, 15, 16, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237435 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(CC(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 11, 11, 11, 11, 21, 21, 21, 11, 1, 1, 2, 2, 2, 1, 1, 1, 11, 11, 11, 21, 21, 11] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 26, 27, 28] set([32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237435 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237435 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237435/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237435 Building REAL300000237436 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237436' /scratch/stefan/7769818/working/building/REAL300000237436 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237436 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237436/0 /scratch/stefan/7769818/working/building/REAL300000237436 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/436 `/scratch/stefan/7769818/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)=CC=C1C(=O)[O-]) `REAL300000237436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237436 none COC1=CC(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 13, 13, 13, 13, 13, 10, 1, 2, 2, 2, 1, 1, 10, 10] 13 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 35, 34, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237436 none COC1=CC(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 10, 10, 10, 10, 10, 10, 1, 1] 13 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 18, 19, 20, 21, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237436 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237436 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237436/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237436 Building REAL300000237437 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237437' /scratch/stefan/7769818/working/building/REAL300000237437 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237437 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237437/0 /scratch/stefan/7769818/working/building/REAL300000237437 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/437 `/scratch/stefan/7769818/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=C(F)C=C(C(=O)[O-])C=C1F)C2=O) `REAL300000237437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237437 none CC1=CC(Cl)=CC2=C1OC(=CC1=C(F)C=C(C(=O)[O-])C=C1F)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1] 3 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237437 none CC1=CC(Cl)=CC2=C1OC(=CC1=C(F)C=C(C(=O)[O-])C=C1F)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2, 1, 1, 1, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 27, 28, 29] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 30, 31]) total number of confs: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237437 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237437 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237437/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237437 Building REAL300000237438 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237438' /scratch/stefan/7769818/working/building/REAL300000237438 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237438 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237438/0 /scratch/stefan/7769818/working/building/REAL300000237438 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/438 `/scratch/stefan/7769818/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CSC(C(=O)[O-])=C1)C2=O) `REAL300000237438.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237438 none CC1=CC(Cl)=CC2=C1OC(=CC1=CSC(C(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 6, 6, 7, 7, 7, 6, 6, 6, 1, 1] 7 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237438 none CC1=CC(Cl)=CC2=C1OC(=CC1=CSC(C(=O)[O-])=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 1, 1, 2, 2, 2, 1, 1, 1, 6, 6] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26] set([12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 27, 28]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237438 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237438 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237438/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237438 Building REAL300000237439 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237439' /scratch/stefan/7769818/working/building/REAL300000237439 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237439 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237439/0 /scratch/stefan/7769818/working/building/REAL300000237439 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/439 `/scratch/stefan/7769818/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)=CC=C1OCC(=O)[O-]) `REAL300000237439.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237439 none CCOC1=CC(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 63, 159, 176, 176, 91, 91, 91, 91, 91, 9, 1, 2, 2, 2, 1, 1, 9, 9, 159, 159] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 38, 37] set([0, 1, 2, 3, 4, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 813 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237439 none CCOC1=CC(C=C2OC3=C(C)C=C(Cl)C=C3C2=O)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 10, 39, 60, 60, 28, 28, 28, 28, 28, 1, 9, 9, 9, 9, 9, 9, 1, 1, 39, 39] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 40, 19, 20, 21, 22] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237439 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237439 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237439/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237439 Building REAL300000237440 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237440' /scratch/stefan/7769818/working/building/REAL300000237440 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237440 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237440/0 /scratch/stefan/7769818/working/building/REAL300000237440 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/440 `/scratch/stefan/7769818/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC(F)=C(C(=O)[O-])C(F)=C1)C2=O) `REAL300000237440.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237440 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC(F)=C(C(=O)[O-])C(F)=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 6 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237440 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC(F)=C(C(=O)[O-])C(F)=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 1, 1, 5, 5, 6, 6, 6, 1, 1, 2, 2, 2, 1, 1, 1, 6, 6] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 27, 28, 29] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 30, 31]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237440 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237440 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237440/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237440 Building REAL300000237441 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237441' /scratch/stefan/7769818/working/building/REAL300000237441 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237441 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237441/0 /scratch/stefan/7769818/working/building/REAL300000237441 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/441 `/scratch/stefan/7769818/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC3=C(C=C(C(=O)[O-])N3)O1)C2=O) `REAL300000237441.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237441 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC3=C(C=C(C(=O)[O-])N3)O1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1] 6 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237441 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC3=C(C=C(C(=O)[O-])N3)O1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 5, 5, 6, 6, 6, 6, 1, 1, 2, 2, 2, 1, 1, 1, 6, 6, 6] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 27, 28, 29] set([32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 30, 31]) total number of confs: 18 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237441 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237441 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237441/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237441 Building REAL300000237442 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237442' /scratch/stefan/7769818/working/building/REAL300000237442 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237442 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237442/0 /scratch/stefan/7769818/working/building/REAL300000237442 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/442 `/scratch/stefan/7769818/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C3OC(C(=O)[O-])=CC3=C1)C2=O) `REAL300000237442.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237442 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C3OC(C(=O)[O-])=CC3=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 5 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237442 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C3OC(C(=O)[O-])=CC3=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 28, 29, 30] set([32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 31]) total number of confs: 12 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237442 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237442 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237442/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237442 Building REAL300000237443 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237443' /scratch/stefan/7769818/working/building/REAL300000237443 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237443 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237443/0 /scratch/stefan/7769818/working/building/REAL300000237443 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/443 `/scratch/stefan/7769818/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CN3C(C(=O)[O-])=CN=C13)C2=O) `REAL300000237443.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237443 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CN3C(C(=O)[O-])=CN=C13)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 7 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237443 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CN3C(C(=O)[O-])=CN=C13)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 2, 2, 2, 1, 1, 1, 7, 7, 7, 7] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 28, 29, 30] set([32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 31]) total number of confs: 14 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237443 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237443 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237443/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237443 Building REAL300000237444 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237444' /scratch/stefan/7769818/working/building/REAL300000237444 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237444 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237444/0 /scratch/stefan/7769818/working/building/REAL300000237444 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/444 `/scratch/stefan/7769818/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=NC3=CC=CC=C3C(C(=O)[O-])=C1C)C2=O) `REAL300000237444.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237444 none CC1=CC(Cl)=CC2=C1OC(=CC1=NC3=CC=CC=C3C(C(=O)[O-])=C1C)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'N.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', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 2, 2, 2] 9 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237444 none CC1=CC(Cl)=CC2=C1OC(=CC1=NC3=CC=CC=C3C(C(=O)[O-])=C1C)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'N.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', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 2, 2, 2, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 25, 26, 30, 31] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237444 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237444 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237444/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237444 Building REAL300000237445 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237445' /scratch/stefan/7769818/working/building/REAL300000237445 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237445 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237445/0 /scratch/stefan/7769818/working/building/REAL300000237445 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/445 `/scratch/stefan/7769818/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CN=C3C=CC(C(=O)[O-])=CN13)C2=O) `REAL300000237445.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237445 none CC1=CC(Cl)=CC2=C1OC(=CC1=CN=C3C=CC(C(=O)[O-])=CN13)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1] 10 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237445 none CC1=CC(Cl)=CC2=C1OC(=CC1=CN=C3C=CC(C(=O)[O-])=CN13)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 2, 2, 2, 1, 1, 1, 10, 10, 10, 10] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 28, 29, 30] set([32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 31]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237445 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237445 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237445/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237445 Building REAL300000237446 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237446' /scratch/stefan/7769818/working/building/REAL300000237446 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237446 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237446/0 /scratch/stefan/7769818/working/building/REAL300000237446 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/446 `/scratch/stefan/7769818/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(N3C=NC(C(=O)[O-])=C3)C=C1)C2=O) `REAL300000237446.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237446 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(N3C=NC(C(=O)[O-])=C3)C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 7, 7, 1, 1] 9 rigid atoms, others: [33, 34, 37, 38, 10, 11, 12, 13, 14, 15, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 16 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237446 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(N3C=NC(C(=O)[O-])=C3)C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 1, 1, 7, 7] 9 rigid atoms, others: [35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 21 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: REAL300000237446 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(N3C=NC(C(=O)[O-])=C3)C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 3, 4, 9, 9, 9, 9, 9, 9, 9, 4, 4, 1, 1, 2, 2, 2, 1, 1, 1, 4, 4, 9, 9, 4, 4] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 25, 26, 30, 31] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237446 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237446 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237446/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237446 Building REAL300000237447 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237447' /scratch/stefan/7769818/working/building/REAL300000237447 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237447 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237447/0 /scratch/stefan/7769818/working/building/REAL300000237447 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/447 `/scratch/stefan/7769818/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(C(=O)[O-])=C1F)C2=O) `REAL300000237447.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237447 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(C(=O)[O-])=C1F)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1] 10 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237447 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=CC(C(=O)[O-])=C1F)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 2, 2, 2, 1, 1, 1, 10, 10, 10] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 26, 27, 28] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237447 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237447 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237447/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237447 Building REAL300000237448 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237448' /scratch/stefan/7769818/working/building/REAL300000237448 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237448 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237448/0 /scratch/stefan/7769818/working/building/REAL300000237448 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/448 `/scratch/stefan/7769818/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(OCC(=O)[O-])C(Cl)=C1)C2=O) `REAL300000237448.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237448 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(OCC(=O)[O-])C(Cl)=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 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] 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: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 10, 43, 61, 61, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 43, 43, 1] 103 rigid atoms, others: [32, 35, 10, 11, 12, 13, 14, 15, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 226 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237448 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(OCC(=O)[O-])C(Cl)=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 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] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 60, 103, 103, 103, 11, 11, 11, 1, 1, 2, 2, 2, 1, 1, 1, 11, 11, 103, 103, 11] 103 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 28, 29, 30] set([32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 31]) total number of confs: 293 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237448 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237448 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237448/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237448 Building REAL300000237449 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237449' /scratch/stefan/7769818/working/building/REAL300000237449 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237449 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237449/0 /scratch/stefan/7769818/working/building/REAL300000237449 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/449 `/scratch/stefan/7769818/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=CC=C3C(=O)[O-])C=C1)C2=O) `REAL300000237449.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237449 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=CC=C3C(=O)[O-])C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.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, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 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] 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: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 4, 5, 5, 5, 7, 7, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 5, 5, 4, 5, 1, 1] 12 rigid atoms, others: [34, 35, 40, 41, 10, 11, 12, 13, 14, 15, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237449 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=CC=C3C(=O)[O-])C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.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, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 1, 1, 1, 1, 5, 5] 12 rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 45 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: REAL300000237449 none CC1=CC(Cl)=CC2=C1OC(=CC1=CC=C(C3=CC=CC=C3C(=O)[O-])C=C1)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.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, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 1, 1, 2, 2, 2, 1, 1, 1, 6, 6, 12, 12, 12, 12, 6, 6] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 32, 26, 27, 31] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237449 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237449 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237449/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237449 Building REAL300000237450 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237450' /scratch/stefan/7769818/working/building/REAL300000237450 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237450 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237450/0 /scratch/stefan/7769818/working/building/REAL300000237450 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/450 `/scratch/stefan/7769818/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=C1OC2=C(C)C=C(Cl)C=C2C1=O) `REAL300000237450.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237450 none COC1=CC(C(=O)[O-])=CC=C1C=C1OC2=C(C)C=C(Cl)C=C2C1=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', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 11, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 2, 2, 2, 1, 1] 7 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 32, 24, 25, 26, 27, 28, 29, 31]) total number of confs: 14 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237450 none COC1=CC(C(=O)[O-])=CC=C1C=C1OC2=C(C)C=C(Cl)C=C2C1=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', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 5, 1, 1, 16, 1, 1, 1, 11, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7] 7 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 27, 28, 29] set([0, 6, 7, 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: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237450 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237450 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237450/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237450 Building REAL300000237451 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237451' /scratch/stefan/7769818/working/building/REAL300000237451 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237451 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237451/0 /scratch/stefan/7769818/working/building/REAL300000237451 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/451 `/scratch/stefan/7769818/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC2=C1OC(=CC1=C3C=C(C(=O)[O-])SC3=CC=C1F)C2=O) `REAL300000237451.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237451 none CC1=CC(Cl)=CC2=C1OC(=CC1=C3C=C(C(=O)[O-])SC3=CC=C1F)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1] 9 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237451 none CC1=CC(Cl)=CC2=C1OC(=CC1=C3C=C(C(=O)[O-])SC3=CC=C1F)C2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 2, 2, 2, 1, 1, 1, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 29, 30, 31] set([32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237451 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237451 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237451/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237451 Building REAL300000237452 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237452' /scratch/stefan/7769818/working/building/REAL300000237452 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237452 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237452/0 /scratch/stefan/7769818/working/building/REAL300000237452 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/452 `/scratch/stefan/7769818/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CC=C1OCC(=O)[O-]) `REAL300000237452.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237452 none COC1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 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, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 39, 39, 39, 15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 120, 201, 201, 201, 71, 71, 71, 39, 15, 15, 1, 1, 1, 39, 39, 201, 201] 201 rigid atoms, others: [32, 33, 7, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 642 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237452 none COC1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 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, 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] 0 hydrogens 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, 9, 9, 39, 39, 39, 17, 39, 39, 39, 1, 1, 1, 1, 9, 28, 38, 38, 3, 3, 3, 1, 5, 5, 39, 17, 39, 1, 1, 28, 28] 201 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 17, 18, 19, 20, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 238 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237452 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237452 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237452/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237452 Building REAL300000237453 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237453' /scratch/stefan/7769818/working/building/REAL300000237453 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237453 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237453/0 /scratch/stefan/7769818/working/building/REAL300000237453 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/453 `/scratch/stefan/7769818/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1) `REAL300000237453.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237453 none O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 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, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1, 21, 21] 21 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 55 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237453 none O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 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, 4, 4, 15, 15, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 4, 4, 21, 21, 21, 1, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 49 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237453 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237453 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237453/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237453 Building REAL300000237454 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237454' /scratch/stefan/7769818/working/building/REAL300000237454 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237454 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237454/0 /scratch/stefan/7769818/working/building/REAL300000237454 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/454 `/scratch/stefan/7769818/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1) `REAL300000237454.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237454 none O=C([O-])CCOC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 197, 201, 165, 101, 74, 101, 101, 42, 42, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 101, 101, 201, 201, 201, 201, 101, 101, 42, 42, 1, 1, 1, 101, 101] 201 rigid atoms, others: [32, 33, 34, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 629 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237454 none O=C([O-])CCOC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 8, 15, 8, 3, 1, 1, 1, 1, 1, 1, 5, 5, 37, 37, 101, 101, 101, 61, 101, 101, 101, 1, 1, 8, 8, 8, 8, 1, 1, 5, 5, 101, 63, 101, 1, 1] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 22, 23, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 330 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237454 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237454 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237454/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237454 Building REAL300000237455 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237455' /scratch/stefan/7769818/working/building/REAL300000237455 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237455 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237455/0 /scratch/stefan/7769818/working/building/REAL300000237455 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/455 `/scratch/stefan/7769818/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1) `REAL300000237455.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237455 none O=C([O-])CCOC1=CC=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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, 196, 201, 168, 53, 53, 53, 53, 53, 21, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 53, 201, 201, 201, 201, 53, 53, 53, 21, 21, 1, 1, 1, 53] 201 rigid atoms, others: [33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 430 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237455 none O=C([O-])CCOC1=CC=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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: [30, 15, 26, 15, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 53, 53, 53, 29, 53, 53, 53, 1, 15, 15, 15, 15, 1, 1, 1, 5, 5, 53, 29, 53, 1] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 23, 28, 29, 30] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 236 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237455 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237455 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237455/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237455 Building REAL300000237456 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237456' /scratch/stefan/7769818/working/building/REAL300000237456 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237456 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237456/0 /scratch/stefan/7769818/working/building/REAL300000237456 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/456 `/scratch/stefan/7769818/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)O2)C=C1) `REAL300000237456.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237456 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 12, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 6, 6, 1, 1, 1, 1, 1, 1, 13, 13, 49, 49, 119, 119, 119, 69, 119, 119, 119, 1, 6, 6, 7, 7, 1, 1, 13, 13, 119, 89, 119, 7, 7] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 385 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237456 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 12, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 119, 201, 119, 201, 201, 119, 119, 119, 119, 43, 43, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 119, 201, 201, 201, 201, 119, 119, 43, 43, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 835 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: REAL300000237456 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 12, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 54, 54, 128, 128, 201, 201, 201, 157, 201, 201, 201, 7, 1, 1, 1, 1, 7, 7, 54, 54, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 24, 25, 26, 27, 36] 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]) total number of confs: 603 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237456 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237456 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237456/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237456 Building REAL300000237457 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237457' /scratch/stefan/7769818/working/building/REAL300000237457 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237457 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237457/0 /scratch/stefan/7769818/working/building/REAL300000237457 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/457 `/scratch/stefan/7769818/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1) `REAL300000237457.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237457 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 192, 55, 55, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 192, 192, 192, 192, 192, 192, 55, 55, 1, 1, 1, 192, 192] 192 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 301 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237457 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 11, 11, 75, 75, 192, 192, 192, 127, 192, 192, 192, 1, 1, 4, 4, 4, 1, 11, 11, 192, 128, 192, 1, 1] 192 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 35, 24, 25, 29, 36] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 504 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237457 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237457 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237457/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237457 Building REAL300000237458 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237458' /scratch/stefan/7769818/working/building/REAL300000237458 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237458 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237458/0 /scratch/stefan/7769818/working/building/REAL300000237458 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/458 `/scratch/stefan/7769818/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=CC(=O)C2=C(F)C=CC=C2Cl)N=N1) `REAL300000237458.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237458 none O=C([O-])CN1C=C(C=CC(=O)C2=C(F)C=CC=C2Cl)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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] 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, 81, 81, 81, 25, 25, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 100, 100, 81, 25, 25, 1, 1, 1] 100 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237458 none O=C([O-])CN1C=C(C=CC(=O)C2=C(F)C=CC=C2Cl)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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] 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: [13, 7, 13, 1, 1, 1, 1, 1, 9, 9, 26, 26, 81, 81, 81, 26, 81, 81, 81, 1, 1, 7, 7, 1, 9, 9, 81, 43, 81] 100 rigid atoms, others: [3, 4, 5, 6, 7, 19, 20, 23] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237458 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237458 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237458/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237458 Building REAL300000237459 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237459' /scratch/stefan/7769818/working/building/REAL300000237459 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237459 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237459/0 /scratch/stefan/7769818/working/building/REAL300000237459 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/459 `/scratch/stefan/7769818/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1) `REAL300000237459.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237459 none O=C([O-])C1=CC=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 35, 35, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 35, 35, 1, 1, 1, 57] 57 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 115 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237459 none O=C([O-])C1=CC=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 57, 57, 57, 54, 57, 57, 57, 1, 1, 1, 1, 6, 6, 57, 57, 57, 1] 57 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 130 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237459 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237459 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237459/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237459 Building REAL300000237460 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237460' /scratch/stefan/7769818/working/building/REAL300000237460 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237460 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237460/0 /scratch/stefan/7769818/working/building/REAL300000237460 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/460 `/scratch/stefan/7769818/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1) `REAL300000237460.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237460 none O=C([O-])C1=CSC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 67, 35, 35, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 35, 35, 1, 1, 1, 67] 67 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 26]) total number of confs: 133 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237460 none O=C([O-])C1=CSC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 47, 47, 67, 67, 67, 51, 67, 67, 67, 1, 1, 11, 11, 67, 67, 67, 1] 67 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237460 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237460 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237460/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237460 Building REAL300000237461 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237461' /scratch/stefan/7769818/working/building/REAL300000237461 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237461 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237461/0 /scratch/stefan/7769818/working/building/REAL300000237461 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/461 `/scratch/stefan/7769818/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CC=C1OCCC(=O)[O-]) `REAL300000237461.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237461 none COC1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 41, 41, 41, 15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 171, 194, 194, 201, 200, 71, 71, 71, 41, 15, 15, 1, 1, 1, 41, 41, 194, 194, 194, 194] 201 rigid atoms, others: [32, 33, 34, 7, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 8, 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: 446 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237461 none COC1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 41, 41, 41, 21, 41, 41, 41, 1, 1, 1, 1, 9, 24, 24, 39, 37, 3, 3, 3, 1, 5, 5, 41, 21, 41, 1, 1, 24, 24, 24, 24] 201 rigid atoms, others: [1, 2, 3, 4, 5, 35, 17, 18, 19, 20, 36, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 252 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237461 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237461 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237461/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237461 Building REAL300000237462 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237462' /scratch/stefan/7769818/working/building/REAL300000237462 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237462 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237462/0 /scratch/stefan/7769818/working/building/REAL300000237462 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/462 `/scratch/stefan/7769818/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C(Cl)=C1) `REAL300000237462.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237462 none O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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] 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, 46, 60, 60, 46, 46, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 46, 46, 1, 1, 1, 60] 60 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 203 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237462 none O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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] 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: [2, 1, 2, 1, 1, 1, 1, 1, 9, 9, 44, 44, 60, 60, 60, 51, 60, 60, 60, 1, 1, 1, 1, 1, 9, 9, 60, 60, 60, 1] 60 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237462 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237462 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237462/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237462 Building REAL300000237463 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237463' /scratch/stefan/7769818/working/building/REAL300000237463 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237463 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237463/0 /scratch/stefan/7769818/working/building/REAL300000237463 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/463 `/scratch/stefan/7769818/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1Cl) `REAL300000237463.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237463 none O=C([O-])C1=CC=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 49, 49, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 49, 49, 1, 1, 1] 111 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 203 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237463 none O=C([O-])C1=CC=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 3, 1, 1, 1, 1, 1, 1, 9, 9, 55, 55, 111, 111, 111, 79, 111, 111, 111, 1, 1, 1, 1, 1, 9, 9, 111, 111, 111] 111 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29]) total number of confs: 337 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237463 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237463 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237463/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237463 Building REAL300000237464 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237464' /scratch/stefan/7769818/working/building/REAL300000237464 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237464 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237464/0 /scratch/stefan/7769818/working/building/REAL300000237464 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/464 `/scratch/stefan/7769818/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CC=C1O) `REAL300000237464.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237464 none O=C([O-])C1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [101, 101, 101, 101, 101, 45, 45, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 101, 45, 45, 1, 1, 1, 101, 101, 202] 202 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 389 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237464 none O=C([O-])C1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 1, 1, 1, 1, 5, 5, 33, 33, 101, 101, 101, 63, 101, 101, 101, 1, 1, 1, 1, 1, 5, 5, 101, 101, 101, 1, 1, 2] 202 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 30]) total number of confs: 335 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237464 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237464 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237464/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237464 Building REAL300000237465 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237465' /scratch/stefan/7769818/working/building/REAL300000237465 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237465 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237465/0 /scratch/stefan/7769818/working/building/REAL300000237465 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/465 `/scratch/stefan/7769818/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=C(F)C=CC=C1Cl) `REAL300000237465.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237465 none CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=C(F)C=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 49, 49, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 71, 71, 71, 49, 49, 1, 1, 1] 71 rigid atoms, others: [33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 149 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237465 none CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=C(F)C=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 43, 43, 71, 71, 71, 63, 71, 71, 71, 2, 2, 2, 1, 2, 2, 2, 1, 9, 9, 71, 71, 71] 71 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 26, 30] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237465 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237465 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237465/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237465 Building REAL300000237466 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237466' /scratch/stefan/7769818/working/building/REAL300000237466 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237466 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237466/0 /scratch/stefan/7769818/working/building/REAL300000237466 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/466 `/scratch/stefan/7769818/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1)C(=O)[O-]) `REAL300000237466.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237466 none CC(OC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 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, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 159, 84, 79, 84, 84, 33, 33, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 201, 201, 201, 201, 201, 201, 201, 84, 84, 33, 33, 1, 1, 1, 84, 84] 201 rigid atoms, others: [32, 33, 34, 9, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 550 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237466 none CC(OC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 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, 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] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 5, 5, 31, 31, 84, 84, 84, 31, 84, 84, 84, 1, 1, 14, 21, 21, 14, 14, 14, 14, 1, 1, 5, 5, 84, 52, 84, 1, 1] 201 rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 19, 20, 36, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 348 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237466 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237466 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237466/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237466 Building REAL300000237467 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237467' /scratch/stefan/7769818/working/building/REAL300000237467 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237467 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237467/0 /scratch/stefan/7769818/working/building/REAL300000237467 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/467 `/scratch/stefan/7769818/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1F) `REAL300000237467.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237467 none O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 92, 92, 92, 44, 44, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 92, 44, 44, 1, 1, 1, 92] 92 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 175 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237467 none O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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] 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: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 39, 39, 92, 92, 92, 41, 92, 92, 92, 1, 1, 1, 1, 1, 6, 6, 92, 60, 92, 1] 92 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 296 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237467 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237467 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237467/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237467 Building REAL300000237468 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237468' /scratch/stefan/7769818/working/building/REAL300000237468 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237468 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237468/0 /scratch/stefan/7769818/working/building/REAL300000237468 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/468 `/scratch/stefan/7769818/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)O1) `REAL300000237468.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237468 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 129, 129, 129, 129, 43, 43, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 129, 201, 201, 129, 129, 43, 43, 1, 1, 1] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 469 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237468 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 11, 31, 11, 1, 1, 1, 1, 1, 1, 12, 12, 58, 58, 129, 129, 129, 90, 129, 129, 129, 1, 12, 11, 1, 1, 12, 12, 129, 93, 129] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 421 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237468 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237468 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237468/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237468 Building REAL300000237469 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237469' /scratch/stefan/7769818/working/building/REAL300000237469 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237469 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237469/0 /scratch/stefan/7769818/working/building/REAL300000237469 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/469 `/scratch/stefan/7769818/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1C(=O)[O-]) `REAL300000237469.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237469 none COC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1C(=O)[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.2', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 1, 1, 1, 1, 11, 1, 1, 15, 1, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 119, 119, 119, 119, 53, 53, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 201, 201, 201, 201, 201, 119, 119, 53, 53, 1, 1, 1, 119] 201 rigid atoms, others: [32, 8, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 713 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237469 none COC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1C(=O)[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.2', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 1, 1, 1, 1, 11, 1, 1, 15, 1, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 42, 42, 119, 119, 119, 71, 119, 119, 119, 1, 1, 1, 3, 3, 4, 4, 4, 1, 1, 6, 6, 119, 119, 119, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 18, 19, 20, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 411 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237469 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237469 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237469/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237469 Building REAL300000237470 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237470' /scratch/stefan/7769818/working/building/REAL300000237470 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237470 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237470/0 /scratch/stefan/7769818/working/building/REAL300000237470 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/470 `/scratch/stefan/7769818/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1) `REAL300000237470.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237470 none O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 90, 90, 90, 50, 50, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 50, 50, 1, 1, 1, 90] 90 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 29]) total number of confs: 183 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237470 none O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 11, 11, 55, 55, 90, 90, 90, 63, 90, 90, 90, 1, 1, 1, 11, 11, 90, 90, 90, 1] 90 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28]) total number of confs: 316 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237470 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237470 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237470/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237470 Building REAL300000237471 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237471' /scratch/stefan/7769818/working/building/REAL300000237471 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237471 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237471/0 /scratch/stefan/7769818/working/building/REAL300000237471 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/471 `/scratch/stefan/7769818/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CC=C1F) `REAL300000237471.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237471 none O=C([O-])C1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 47, 47, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 47, 47, 1, 1, 1, 107, 107] 107 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 199 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237471 none O=C([O-])C1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 5, 5, 37, 37, 107, 107, 107, 66, 107, 107, 107, 1, 1, 1, 1, 1, 5, 5, 107, 69, 107, 1, 1] 107 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27]) total number of confs: 291 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237471 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237471 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237471/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237471 Building REAL300000237472 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237472' /scratch/stefan/7769818/working/building/REAL300000237472 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237472 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237472/0 /scratch/stefan/7769818/working/building/REAL300000237472 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/472 `/scratch/stefan/7769818/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1) `REAL300000237472.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237472 none O=C([O-])CC1=CC=C(C=CC(=O)C2=C(F)C=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 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, 60, 51, 64, 64, 50, 50, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 64, 50, 50, 1, 1, 1, 64, 64] 64 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 11, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 210 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237472 none O=C([O-])CC1=CC=C(C=CC(=O)C2=C(F)C=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 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, 2, 4, 1, 1, 1, 1, 1, 1, 6, 6, 31, 31, 64, 64, 64, 50, 64, 64, 64, 1, 1, 2, 2, 1, 1, 6, 6, 64, 62, 64, 1, 1] 64 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 20, 21, 24, 25, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 205 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237472 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237472 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237472/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237472 Building REAL300000237473 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237473' /scratch/stefan/7769818/working/building/REAL300000237473 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237473 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237473/0 /scratch/stefan/7769818/working/building/REAL300000237473 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/473 `/scratch/stefan/7769818/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(Br)=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1) `REAL300000237473.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237473 none O=C([O-])C1=CC(Br)=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 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, 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, 33, 33, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 33, 33, 1, 1, 1, 59] 59 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 29]) total number of confs: 119 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237473 none O=C([O-])C1=CC(Br)=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 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, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 29, 29, 59, 59, 59, 29, 59, 59, 59, 1, 1, 1, 5, 5, 59, 59, 59, 1] 59 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28]) total number of confs: 243 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237473 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237473 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237473/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237473 Building REAL300000237474 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237474' /scratch/stefan/7769818/working/building/REAL300000237474 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237474 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237474/0 /scratch/stefan/7769818/working/building/REAL300000237474 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/474 `/scratch/stefan/7769818/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)S1) `REAL300000237474.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237474 none O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 35, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 35, 35, 1, 1, 1] 63 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237474 none O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 45, 45, 63, 63, 63, 61, 63, 63, 63, 1, 1, 1, 11, 11, 63, 63, 63] 63 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237474 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237474 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237474/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237474 Building REAL300000237475 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237475' /scratch/stefan/7769818/working/building/REAL300000237475 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237475 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237475/0 /scratch/stefan/7769818/working/building/REAL300000237475 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/475 `/scratch/stefan/7769818/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1) `REAL300000237475.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237475 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 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 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 108, 92, 65, 108, 108, 51, 51, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 108, 108, 51, 51, 1, 1, 1, 108, 108] 108 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 419 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237475 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 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 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [13, 3, 13, 3, 1, 1, 1, 1, 1, 1, 5, 5, 43, 43, 108, 108, 108, 84, 108, 108, 108, 1, 1, 3, 3, 1, 1, 5, 5, 108, 108, 108, 1, 1] 108 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 21, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 337 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237475 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237475 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237475/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237475 Building REAL300000237476 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237476' /scratch/stefan/7769818/working/building/REAL300000237476 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237476 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237476/0 /scratch/stefan/7769818/working/building/REAL300000237476 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/476 `/scratch/stefan/7769818/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1F) `REAL300000237476.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237476 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 131, 131, 131, 131, 52, 52, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 52, 52, 1, 1, 1, 131] 131 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 231 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237476 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 62, 62, 131, 131, 131, 91, 131, 131, 131, 1, 1, 1, 1, 11, 11, 131, 95, 131, 1] 131 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 357 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237476 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237476 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237476/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237476 Building REAL300000237477 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237477' /scratch/stefan/7769818/working/building/REAL300000237477 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237477 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237477/0 /scratch/stefan/7769818/working/building/REAL300000237477 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/477 `/scratch/stefan/7769818/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NNC2=CC=CC(C=CC(=O)C3=C(F)C=CC=C3Cl)=C21) `REAL300000237477.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237477 none O=C([O-])C1=NNC2=CC=CC(C=CC(=O)C3=C(F)C=CC=C3Cl)=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 31, 31, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 31, 31, 1, 1, 1] 49 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237477 none O=C([O-])C1=NNC2=CC=CC(C=CC(=O)C3=C(F)C=CC=C3Cl)=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 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 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, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 27, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 9, 9, 49, 49, 49] 49 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27] set([0, 32, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237477 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237477 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237477/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237477 Building REAL300000237478 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237478' /scratch/stefan/7769818/working/building/REAL300000237478 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237478 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237478/0 /scratch/stefan/7769818/working/building/REAL300000237478 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/478 `/scratch/stefan/7769818/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C=C2)C=C1) `REAL300000237478.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237478 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 7, 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 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 30, 30, 30, 17, 30, 30, 30, 1, 1, 3, 3, 3, 3, 1, 1, 3, 3, 30, 25, 30, 1, 1, 3, 3] 44 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 113 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237478 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 7, 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 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 30, 44, 30, 44, 44, 28, 28, 30, 30, 28, 28, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 44, 44, 44, 44, 30, 30, 28, 28, 1, 1, 1, 30, 30, 44, 44] 44 rigid atoms, others: [33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 209 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: REAL300000237478 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 7, 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 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 5, 5, 23, 23, 44, 44, 44, 33, 44, 44, 44, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 44, 44, 44, 3, 3, 1, 1] 44 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 25, 26, 27, 28, 39] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237478 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237478 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237478/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237478 Building REAL300000237479 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237479' /scratch/stefan/7769818/working/building/REAL300000237479 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237479 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237479/0 /scratch/stefan/7769818/working/building/REAL300000237479 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/479 `/scratch/stefan/7769818/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2NC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C2=C1) `REAL300000237479.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237479 none O=C([O-])C1=CC=C2NC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 91, 91, 91, 91, 91, 35, 35, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 91, 35, 35, 1, 1, 1, 91] 91 rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237479 none O=C([O-])C1=CC=C2NC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 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] 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, 11, 11, 51, 51, 91, 91, 91, 79, 91, 91, 91, 1, 1, 1, 1, 1, 1, 11, 11, 91, 91, 91, 1] 91 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 22, 23, 24, 25, 26, 27] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237479 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237479 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237479/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237479 Building REAL300000237480 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237480' /scratch/stefan/7769818/working/building/REAL300000237480 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237480 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237480/0 /scratch/stefan/7769818/working/building/REAL300000237480 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/480 `/scratch/stefan/7769818/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=N1) `REAL300000237480.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237480 none O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 42, 25, 25, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 25, 25, 1, 1, 1, 42] 42 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 28]) total number of confs: 97 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237480 none O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 29, 29, 42, 42, 42, 29, 42, 42, 42, 1, 1, 1, 1, 5, 5, 42, 42, 42, 1] 42 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237480 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237480 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237480/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237480 Building REAL300000237481 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237481' /scratch/stefan/7769818/working/building/REAL300000237481 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237481 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237481/0 /scratch/stefan/7769818/working/building/REAL300000237481 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/481 `/scratch/stefan/7769818/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1O) `REAL300000237481.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237481 none O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [83, 83, 83, 83, 83, 83, 45, 45, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 45, 45, 1, 1, 1, 83, 166] 166 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 329 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237481 none O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 45, 45, 83, 83, 83, 59, 83, 83, 83, 1, 1, 1, 1, 1, 6, 6, 83, 61, 83, 1, 2] 166 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 30]) total number of confs: 228 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237481 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237481 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237481/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237481 Building REAL300000237482 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237482' /scratch/stefan/7769818/working/building/REAL300000237482 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237482 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237482/0 /scratch/stefan/7769818/working/building/REAL300000237482 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/482 `/scratch/stefan/7769818/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1C(=O)[O-]) `REAL300000237482.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237482 none CC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 49, 49, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 110, 111, 111, 111, 111, 111, 111, 111, 49, 49, 1, 1, 1, 111] 111 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 212 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237482 none CC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 39, 39, 111, 111, 111, 71, 111, 111, 111, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 5, 5, 111, 90, 111, 1] 111 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 17, 18, 19, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 336 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237482 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237482 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237482/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237482 Building REAL300000237483 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237483' /scratch/stefan/7769818/working/building/REAL300000237483 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237483 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237483/0 /scratch/stefan/7769818/working/building/REAL300000237483 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/483 `/scratch/stefan/7769818/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)SC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1) `REAL300000237483.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237483 none O=C([O-])C1=C(Cl)SC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 142, 142, 49, 49, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 142, 49, 49, 1, 1, 1, 142] 142 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 26]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237483 none O=C([O-])C1=C(Cl)SC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 12, 86, 86, 142, 142, 142, 87, 142, 142, 142, 1, 12, 13, 142, 124, 142, 1] 142 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 501 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237483 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237483 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237483/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237483 Building REAL300000237484 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237484' /scratch/stefan/7769818/working/building/REAL300000237484 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237484 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237484/0 /scratch/stefan/7769818/working/building/REAL300000237484 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/484 `/scratch/stefan/7769818/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=C(F)C=CC=C2Cl)O1) `REAL300000237484.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237484 none CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=C(F)C=CC=C2Cl)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 115, 115, 115, 115, 115, 46, 46, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 46, 46, 1, 1, 1] 115 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 208 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237484 none CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=C(F)C=CC=C2Cl)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 3, 3, 1, 1, 1, 11, 11, 56, 56, 115, 115, 115, 115, 115, 115, 115, 1, 2, 2, 2, 1, 11, 11, 115, 115, 115] 115 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 20, 24] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237484 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237484 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237484/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237484 Building REAL300000237485 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237485' /scratch/stefan/7769818/working/building/REAL300000237485 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237485 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237485/0 /scratch/stefan/7769818/working/building/REAL300000237485 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/485 `/scratch/stefan/7769818/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)S2)C=C1) `REAL300000237485.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237485 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 7, 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: [7, 1, 7, 1, 6, 6, 1, 1, 1, 1, 1, 1, 11, 11, 77, 77, 171, 171, 171, 120, 171, 171, 171, 1, 6, 6, 7, 7, 1, 1, 11, 11, 171, 130, 171, 7, 7] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 511 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237485 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 7, 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, 171, 201, 171, 201, 201, 171, 171, 171, 171, 46, 46, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 171, 201, 201, 201, 201, 171, 171, 46, 46, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 533 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: REAL300000237485 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 58, 58, 153, 153, 201, 201, 201, 187, 201, 201, 201, 7, 1, 1, 1, 1, 8, 7, 58, 58, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 24, 25, 26, 27, 36] 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]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237485 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237485 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237485/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237485 Building REAL300000237486 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237486' /scratch/stefan/7769818/working/building/REAL300000237486 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237486 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237486/0 /scratch/stefan/7769818/working/building/REAL300000237486 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/486 `/scratch/stefan/7769818/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=C(F)C=CC=C1Cl) `REAL300000237486.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237486 none CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=C(F)C=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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, 40, 40, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 40, 40, 1, 1, 1] 69 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237486 none CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=C(F)C=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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, 10, 10, 49, 49, 69, 69, 69, 65, 69, 69, 69, 2, 2, 2, 1, 10, 10, 69, 69, 69] 69 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237486 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237486 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237486/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237486 Building REAL300000237487 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237487' /scratch/stefan/7769818/working/building/REAL300000237487 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237487 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237487/0 /scratch/stefan/7769818/working/building/REAL300000237487 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/487 `/scratch/stefan/7769818/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1) `REAL300000237487.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237487 none O=C([O-])C1=CN=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 35, 35, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 35, 35, 1, 1, 1, 57] 57 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 28]) total number of confs: 115 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237487 none O=C([O-])C1=CN=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 57, 57, 57, 47, 57, 57, 57, 1, 1, 1, 6, 6, 57, 57, 57, 1] 57 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237487 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237487 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237487/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237487 Building REAL300000237488 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237488' /scratch/stefan/7769818/working/building/REAL300000237488 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237488 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237488/0 /scratch/stefan/7769818/working/building/REAL300000237488 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/488 `/scratch/stefan/7769818/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)S2)=C1) `REAL300000237488.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237488 none O=C([O-])C1=CC=CC(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 14, 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, 7, 7, 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: [13, 13, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 11, 11, 40, 40, 114, 114, 114, 40, 114, 114, 114, 1, 13, 12, 13, 13, 1, 1, 11, 11, 114, 64, 114, 13] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 388 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237488 none O=C([O-])C1=CC=CC(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 14, 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, 7, 7, 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: [201, 201, 201, 201, 201, 201, 201, 114, 114, 114, 114, 25, 25, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 114, 201, 201, 201, 201, 114, 114, 25, 25, 1, 1, 1, 201] 201 rigid atoms, others: [33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 313 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: REAL300000237488 none O=C([O-])C1=CC=CC(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 14, 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, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 91, 91, 140, 140, 201, 201, 201, 140, 201, 201, 201, 13, 1, 1, 1, 1, 13, 13, 91, 91, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 36] 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: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237488 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237488 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237488/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237488 Building REAL300000237489 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237489' /scratch/stefan/7769818/working/building/REAL300000237489 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237489 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237489/0 /scratch/stefan/7769818/working/building/REAL300000237489 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/489 `/scratch/stefan/7769818/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=C(F)C=CC=C1Cl) `REAL300000237489.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237489 none COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=C(F)C=CC=C1Cl 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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 178, 178, 178, 178, 178, 178, 178, 59, 59, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 178, 178, 178, 178, 178, 176, 59, 59, 1, 1, 1] 178 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 294 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237489 none COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=C(F)C=CC=C1Cl 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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 11, 11, 81, 81, 178, 178, 178, 81, 178, 178, 178, 3, 3, 3, 1, 1, 1, 11, 11, 178, 136, 178] 178 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]) total number of confs: 640 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237489 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237489 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237489/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237489 Building REAL300000237490 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237490' /scratch/stefan/7769818/working/building/REAL300000237490 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237490 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237490/0 /scratch/stefan/7769818/working/building/REAL300000237490 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/490 `/scratch/stefan/7769818/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2SC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C2=C1) `REAL300000237490.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237490 none O=C([O-])C1=CC=C2SC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 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 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 98, 98, 98, 98, 98, 98, 42, 42, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 42, 42, 1, 1, 1, 98] 98 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 32, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 177 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237490 none O=C([O-])C1=CC=C2SC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 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 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 62, 62, 98, 98, 98, 86, 98, 98, 98, 1, 1, 1, 1, 1, 11, 11, 98, 98, 98, 1] 98 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31]) total number of confs: 271 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237490 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237490 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237490/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237490 Building REAL300000237491 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237491' /scratch/stefan/7769818/working/building/REAL300000237491 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237491 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237491/0 /scratch/stefan/7769818/working/building/REAL300000237491 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/491 `/scratch/stefan/7769818/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Br)C(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1) `REAL300000237491.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237491 none O=C([O-])C1=CC=C(Br)C(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 72, 72, 72, 49, 49, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 49, 49, 1, 1, 1, 72] 72 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 29]) total number of confs: 152 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237491 none O=C([O-])C1=CC=C(Br)C(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 9, 9, 48, 48, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 9, 9, 72, 72, 72, 1] 72 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237491 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237491 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237491/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237491 Building REAL300000237492 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237492' /scratch/stefan/7769818/working/building/REAL300000237492 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237492 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237492/0 /scratch/stefan/7769818/working/building/REAL300000237492 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/492 `/scratch/stefan/7769818/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C([N+](=O)[O-])=C1) `REAL300000237492.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237492 none O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 50, 51, 51, 41, 41, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51, 41, 41, 1, 1, 1, 51] 51 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237492 none O=C([O-])C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 7, 7, 31, 31, 51, 51, 51, 31, 51, 51, 51, 1, 1, 2, 2, 1, 1, 1, 7, 7, 51, 51, 51, 1] 51 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 23, 24, 25, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237492 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237492 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237492/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237492 Building REAL300000237493 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237493' /scratch/stefan/7769818/working/building/REAL300000237493 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237493 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237493/0 /scratch/stefan/7769818/working/building/REAL300000237493 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/493 `/scratch/stefan/7769818/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1) `REAL300000237493.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237493 none O=C([O-])CC1=CC=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 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 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, 91, 91, 73, 91, 91, 49, 49, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 91, 131, 131, 73, 91, 91, 49, 49, 1, 1, 1, 91] 131 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 471 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237493 none O=C([O-])CC1=CC=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 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 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 37, 37, 91, 91, 91, 59, 91, 91, 91, 1, 2, 2, 1, 1, 1, 6, 6, 91, 71, 91, 1] 131 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 21, 24, 25, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 274 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237493 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237493 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237493/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237493 Building REAL300000237494 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237494' /scratch/stefan/7769818/working/building/REAL300000237494 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237494 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237494/0 /scratch/stefan/7769818/working/building/REAL300000237494 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/494 `/scratch/stefan/7769818/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CC=C1C(=O)[O-]) `REAL300000237494.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237494 none COC1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [183, 141, 141, 141, 60, 60, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 183, 183, 183, 183, 183, 141, 60, 60, 1, 1, 1, 141, 141] 183 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 517 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237494 none COC1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 6, 6, 46, 46, 141, 141, 141, 81, 141, 141, 141, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 6, 6, 141, 83, 141, 1, 1] 183 rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 17, 18, 19, 20, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 391 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237494 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237494 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237494/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237494 Building REAL300000237495 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237495' /scratch/stefan/7769818/working/building/REAL300000237495 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237495 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237495/0 /scratch/stefan/7769818/working/building/REAL300000237495 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/495 `/scratch/stefan/7769818/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C(F)=C1) `REAL300000237495.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237495 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 25, 25, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 25, 25, 1, 1, 1, 35] 35 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237495 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 10, 10, 21, 21, 35, 35, 35, 28, 35, 35, 35, 1, 1, 1, 1, 10, 10, 35, 35, 35, 1] 35 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237495 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237495 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237495/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237495 Building REAL300000237496 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237496' /scratch/stefan/7769818/working/building/REAL300000237496 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237496 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237496/0 /scratch/stefan/7769818/working/building/REAL300000237496 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/496 `/scratch/stefan/7769818/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C=C2)=C1) `REAL300000237496.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237496 none O=C([O-])CC1=CC=CC(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 33, 33, 105, 105, 105, 61, 105, 105, 105, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 5, 5, 105, 89, 105, 1, 1, 3] 201 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 40, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 42]) total number of confs: 377 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237496 none O=C([O-])CC1=CC=CC(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 153, 153, 153, 153, 153, 75, 75, 105, 105, 43, 43, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 105, 105, 153, 201, 201, 153, 153, 153, 105, 105, 43, 43, 1, 1, 1, 105, 105, 153] 201 rigid atoms, others: [37, 38, 39, 15, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42]) total number of confs: 689 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: REAL300000237496 none O=C([O-])CC1=CC=CC(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 9, 9, 59, 59, 153, 153, 153, 119, 153, 153, 153, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 9, 9, 153, 145, 153, 3, 3, 1] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 42, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 433 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237496 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237496 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237496/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237496 Building REAL300000237497 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237497' /scratch/stefan/7769818/working/building/REAL300000237497 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237497 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237497/0 /scratch/stefan/7769818/working/building/REAL300000237497 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/497 `/scratch/stefan/7769818/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CS1) `REAL300000237497.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237497 none O=C([O-])C1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 35, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 35, 35, 1, 1, 1, 53] 53 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 26]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237497 none O=C([O-])C1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 33, 33, 53, 53, 53, 47, 53, 53, 53, 1, 1, 1, 6, 6, 53, 53, 53, 1] 53 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237497 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237497 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237497/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237497 Building REAL300000237498 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237498' /scratch/stefan/7769818/working/building/REAL300000237498 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237498 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237498/0 /scratch/stefan/7769818/working/building/REAL300000237498 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/498 `/scratch/stefan/7769818/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CC=C1OCC(=O)[O-]) `REAL300000237498.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237498 none CCOC1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 68, 39, 39, 39, 15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 129, 198, 200, 200, 77, 77, 77, 77, 77, 39, 15, 15, 1, 1, 1, 39, 39, 198, 198] 201 rigid atoms, others: [34, 35, 36, 8, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 679 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237498 none CCOC1=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 5, 5, 9, 9, 39, 39, 39, 17, 39, 39, 39, 1, 1, 1, 1, 7, 21, 38, 38, 5, 5, 5, 5, 5, 1, 5, 5, 39, 17, 39, 1, 1, 21, 21] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 19, 20, 21, 38, 37, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 259 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237498 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237498 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237498/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237498 Building REAL300000237499 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237499' /scratch/stefan/7769818/working/building/REAL300000237499 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237499 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237499/0 /scratch/stefan/7769818/working/building/REAL300000237499 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/499 `/scratch/stefan/7769818/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1F) `REAL300000237499.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237499 none O=C([O-])C1=C(F)C=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 35, 51, 35, 51, 51, 51, 35, 35, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 35, 35, 1, 1, 1, 51] 51 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 227 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237499 none O=C([O-])C1=C(F)C=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 21, 21, 51, 51, 51, 39, 51, 51, 51, 1, 1, 1, 1, 3, 3, 51, 51, 51, 1] 51 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237499 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237499 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237499/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237499 Building REAL300000237500 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237500' /scratch/stefan/7769818/working/building/REAL300000237500 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237500 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237500/0 /scratch/stefan/7769818/working/building/REAL300000237500 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/500 `/scratch/stefan/7769818/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=C(C=CC(=O)C3=C(F)C=CC=C3Cl)O2)N1) `REAL300000237500.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237500 none O=C([O-])C1=CC2=C(C=C(C=CC(=O)C3=C(F)C=CC=C3Cl)O2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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, 35, 35, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 35, 35, 1, 1, 1, 55] 55 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237500 none O=C([O-])C1=CC2=C(C=C(C=CC(=O)C3=C(F)C=CC=C3Cl)O2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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, 12, 12, 32, 32, 55, 55, 55, 47, 55, 55, 55, 1, 1, 1, 1, 12, 12, 55, 55, 55, 1] 55 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237500 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237500 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237500/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237500 Building REAL300000237501 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237501' /scratch/stefan/7769818/working/building/REAL300000237501 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237501 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237501/0 /scratch/stefan/7769818/working/building/REAL300000237501 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/501 `/scratch/stefan/7769818/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC(C=CC(=O)C3=C(F)C=CC=C3Cl)=CC=C2O1) `REAL300000237501.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237501 none O=C([O-])C1=CC2=CC(C=CC(=O)C3=C(F)C=CC=C3Cl)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 33, 33, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 33, 33, 1, 1, 1, 49, 49] 49 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 11, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 107 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237501 none O=C([O-])C1=CC2=CC(C=CC(=O)C3=C(F)C=CC=C3Cl)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 6, 6, 29, 29, 49, 49, 49, 29, 49, 49, 49, 1, 1, 1, 1, 1, 1, 6, 6, 49, 49, 49, 1, 1] 49 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237501 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237501 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237501/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237501 Building REAL300000237502 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237502' /scratch/stefan/7769818/working/building/REAL300000237502 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237502 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237502/0 /scratch/stefan/7769818/working/building/REAL300000237502 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/502 `/scratch/stefan/7769818/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2C(C=CC(=O)C3=C(F)C=CC=C3Cl)=CC=CN12) `REAL300000237502.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237502 none O=C([O-])C1=CN=C2C(C=CC(=O)C3=C(F)C=CC=C3Cl)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 42, 42, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 42, 42, 1, 1, 1, 80, 80, 80] 80 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 11, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237502 none O=C([O-])C1=CN=C2C(C=CC(=O)C3=C(F)C=CC=C3Cl)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 48, 48, 80, 80, 80, 66, 80, 80, 80, 1, 1, 1, 1, 1, 11, 11, 80, 80, 80, 1, 1, 1] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237502 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237502 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237502/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237502 Building REAL300000237503 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237503' /scratch/stefan/7769818/working/building/REAL300000237503 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237503 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237503/0 /scratch/stefan/7769818/working/building/REAL300000237503 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/503 `/scratch/stefan/7769818/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=C(F)C=CC=C1Cl) `REAL300000237503.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237503 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=C(F)C=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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 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, 75, 75, 75, 75, 75, 75, 75, 75, 42, 42, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 75, 75, 42, 42, 1, 1, 1] 75 rigid atoms, others: [35, 36, 37, 16, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 157 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237503 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=C(F)C=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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 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, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 55, 55, 75, 75, 75, 75, 75, 75, 75, 2, 2, 2, 1, 1, 1, 1, 10, 10, 75, 75, 75] 75 rigid atoms, others: [0, 1, 2, 3, 32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([33, 34, 35, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 36]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237503 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237503 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237503/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237503 Building REAL300000237504 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237504' /scratch/stefan/7769818/working/building/REAL300000237504 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237504 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237504/0 /scratch/stefan/7769818/working/building/REAL300000237504 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/504 `/scratch/stefan/7769818/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN2C(C=CC(=O)C3=C(F)C=CC=C3Cl)=CN=C2C=C1) `REAL300000237504.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237504 none O=C([O-])C1=CN2C(C=CC(=O)C3=C(F)C=CC=C3Cl)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 101, 101, 101, 40, 40, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 101, 101, 40, 40, 1, 1, 1, 101, 101, 101] 101 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 32, 30, 31]) total number of confs: 178 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237504 none O=C([O-])C1=CN2C(C=CC(=O)C3=C(F)C=CC=C3Cl)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 12, 66, 66, 101, 101, 101, 66, 101, 101, 101, 1, 1, 1, 1, 1, 1, 12, 12, 101, 101, 101, 1, 1, 1] 101 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29]) total number of confs: 360 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237504 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237504 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237504/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237504 Building REAL300000237505 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237505' /scratch/stefan/7769818/working/building/REAL300000237505 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237505 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237505/0 /scratch/stefan/7769818/working/building/REAL300000237505 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/505 `/scratch/stefan/7769818/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C=C2)C=N1) `REAL300000237505.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237505 none O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 36, 36, 73, 73, 73, 55, 73, 73, 73, 1, 1, 6, 6, 6, 1, 1, 5, 5, 73, 65, 73, 1, 1, 6] 86 rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 36]) total number of confs: 219 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237505 none O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 86, 86, 73, 70, 73, 73, 40, 40, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 73, 73, 86, 86, 86, 73, 73, 40, 40, 1, 1, 1, 73, 73, 86] 86 rigid atoms, others: [32, 33, 12, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 197 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: REAL300000237505 none O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 17, 17, 60, 60, 86, 86, 86, 80, 86, 86, 86, 6, 6, 1, 1, 1, 6, 6, 17, 17, 86, 86, 86, 6, 6, 1] 86 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25, 26, 36] set([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: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237505 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237505 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237505/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237505 Building REAL300000237506 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237506' /scratch/stefan/7769818/working/building/REAL300000237506 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237506 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237506/0 /scratch/stefan/7769818/working/building/REAL300000237506 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/506 `/scratch/stefan/7769818/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1F) `REAL300000237506.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237506 none O=C([O-])C1=CC=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 147, 147, 147, 147, 49, 49, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 147, 147, 147, 147, 147, 49, 49, 1, 1, 1] 147 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 239 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237506 none O=C([O-])C1=CC=CC(C=CC(=O)C2=C(F)C=CC=C2Cl)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 84, 84, 147, 147, 147, 112, 147, 147, 147, 1, 1, 1, 1, 1, 11, 11, 147, 117, 147] 147 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29]) total number of confs: 395 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237506 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237506 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237506/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237506 Building REAL300000237507 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237507' /scratch/stefan/7769818/working/building/REAL300000237507 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237507 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237507/0 /scratch/stefan/7769818/working/building/REAL300000237507 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/507 `/scratch/stefan/7769818/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1Cl) `REAL300000237507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237507 none O=C([O-])COC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 168, 67, 67, 67, 67, 23, 23, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 201, 201, 67, 67, 23, 23, 1, 1, 1, 67] 201 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 472 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237507 none O=C([O-])COC1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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, 25, 39, 7, 1, 1, 1, 1, 1, 1, 5, 5, 23, 23, 67, 67, 67, 39, 67, 67, 67, 1, 1, 1, 25, 25, 1, 1, 5, 5, 67, 67, 67, 1] 201 rigid atoms, others: [33, 4, 5, 6, 7, 8, 9, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 346 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237507 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237507 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237507/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237507 Building REAL300000237508 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237508' /scratch/stefan/7769818/working/building/REAL300000237508 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237508 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237508/0 /scratch/stefan/7769818/working/building/REAL300000237508 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/508 `/scratch/stefan/7769818/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNS(=O)(=O)C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1) `REAL300000237508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237508 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 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] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 182, 171, 97, 58, 97, 97, 33, 97, 97, 32, 32, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 97, 97, 182, 182, 171, 97, 97, 32, 32, 1, 1, 1, 97, 97] 182 rigid atoms, others: [33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 902 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237508 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 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] 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: [9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 31, 31, 97, 97, 97, 55, 97, 97, 97, 1, 1, 9, 9, 5, 1, 1, 6, 6, 97, 58, 97, 1, 1] 182 rigid atoms, others: [36, 5, 8, 9, 10, 11, 12, 24, 25, 29, 30, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 299 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237508 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237508 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237508/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237508 Building REAL300000237509 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237509' /scratch/stefan/7769818/working/building/REAL300000237509 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237509 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237509/0 /scratch/stefan/7769818/working/building/REAL300000237509 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/509 `/scratch/stefan/7769818/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC=C1C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1) `REAL300000237509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237509 none O=C([O-])C1=CC=CC=C1C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 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 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 5, 4, 4, 3, 4, 4, 1, 1, 1, 1, 1, 1, 6, 6, 45, 45, 96, 96, 96, 65, 96, 96, 96, 1, 1, 4, 3, 4, 4, 1, 1, 6, 6, 96, 69, 96, 1, 1] 131 rigid atoms, others: [32, 38, 39, 8, 9, 10, 11, 12, 13, 25, 26, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 276 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237509 none O=C([O-])C1=CC=CC=C1C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 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 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, 121, 131, 131, 93, 77, 96, 96, 49, 49, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96, 131, 131, 131, 131, 96, 96, 49, 49, 1, 1, 1, 96, 96] 131 rigid atoms, others: [35, 36, 37, 15, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 392 number of broken/clashed sets: 9 ./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: REAL300000237509 none O=C([O-])C1=CC=CC=C1C1=CC=C(C=CC(=O)C2=C(F)C=CC=C2Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 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 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 2, 17, 17, 73, 73, 131, 131, 131, 108, 131, 131, 131, 4, 4, 1, 1, 1, 1, 4, 4, 17, 17, 131, 117, 131, 4, 4] 131 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 370 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237509 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237509 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237509/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237509 Building REAL300000237510 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237510' /scratch/stefan/7769818/working/building/REAL300000237510 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237510 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237510/0 /scratch/stefan/7769818/working/building/REAL300000237510 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/510 `/scratch/stefan/7769818/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=C(F)C=CC=C1Cl) `REAL300000237510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237510 none COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=C(F)C=CC=C1Cl 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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 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, 131, 131, 131, 131, 131, 131, 131, 57, 57, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 131, 57, 57, 1, 1, 1] 131 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 241 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237510 none COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=C(F)C=CC=C1Cl 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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 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, 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: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 11, 11, 67, 67, 131, 131, 131, 110, 131, 131, 131, 3, 3, 3, 1, 1, 1, 11, 11, 131, 128, 131] 131 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 26, 27, 28] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 354 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237510 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237510 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237510/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237510 Building REAL300000237511 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237511' /scratch/stefan/7769818/working/building/REAL300000237511 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237511 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237511/0 /scratch/stefan/7769818/working/building/REAL300000237511 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/511 `/scratch/stefan/7769818/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C(F)=CC=C2S1) `REAL300000237511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237511 none O=C([O-])C1=CC2=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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] 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, 43, 43, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 97, 97, 97, 43, 43, 1, 1, 1, 97, 97] 97 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 31]) total number of confs: 173 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237511 none O=C([O-])C1=CC2=C(C=CC(=O)C3=C(F)C=CC=C3Cl)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 15, 1, 1, 1, 1, 16, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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] 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: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 57, 57, 97, 97, 97, 83, 97, 97, 97, 1, 1, 1, 1, 1, 1, 1, 11, 11, 97, 97, 97, 1, 1] 97 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30]) total number of confs: 275 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237511 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237511 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237511/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237511 Building REAL300000237512 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237512' /scratch/stefan/7769818/working/building/REAL300000237512 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237512 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237512/0 /scratch/stefan/7769818/working/building/REAL300000237512 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/512 `/scratch/stefan/7769818/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1OCC(=O)[O-]) `REAL300000237512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237512 none COC1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 51, 112, 115, 115, 17, 17, 17, 7, 1, 1, 1, 1, 1, 7, 7, 112, 112] 115 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 36, 37, 35, 34, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 362 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237512 none COC1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 11, 54, 81, 81, 4, 4, 4, 1, 7, 7, 7, 7, 7, 1, 1, 54, 54] 115 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 17, 18, 19, 20, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 293 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237512 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237512 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237512/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237512 Building REAL300000237513 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237513' /scratch/stefan/7769818/working/building/REAL300000237513 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237513 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237513/0 /scratch/stefan/7769818/working/building/REAL300000237513 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/513 `/scratch/stefan/7769818/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1) `REAL300000237513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237513 none O=C([O-])COC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 11, 3, 2, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 6, 6, 1, 1, 1, 1, 1, 6, 6] 22 rigid atoms, others: [8, 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, 32, 33, 21, 22, 23, 24, 25, 26]) total number of confs: 84 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237513 none O=C([O-])COC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 16, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 13, 13, 1, 1, 6, 6, 6, 6, 6, 1, 1] 22 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 21, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 64 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237513 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237513 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237513/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237513 Building REAL300000237514 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237514' /scratch/stefan/7769818/working/building/REAL300000237514 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237514 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237514/0 /scratch/stefan/7769818/working/building/REAL300000237514 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/514 `/scratch/stefan/7769818/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1) `REAL300000237514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237514 none O=C([O-])CCOC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 39, 32, 14, 3, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 40, 40, 32, 32, 7, 7, 1, 1, 1, 1, 1, 7, 7] 40 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 153 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237514 none O=C([O-])CCOC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 22, 13, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 17, 17, 13, 13, 1, 1, 7, 7, 7, 7, 7, 1, 1] 40 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 22, 23, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 99 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237514 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237514 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237514/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237514 Building REAL300000237515 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237515' /scratch/stefan/7769818/working/building/REAL300000237515 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237515 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237515/0 /scratch/stefan/7769818/working/building/REAL300000237515 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/515 `/scratch/stefan/7769818/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1)C(=O)[O-]) `REAL300000237515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237515 none CC(OC1=CC=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 60, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 90, 90, 90, 90, 90, 90, 90, 7, 7, 7, 1, 1, 1, 1, 1, 7] 90 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 244 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237515 none CC(OC1=CC=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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: [40, 13, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 40, 49, 49, 40, 40, 40, 40, 1, 1, 1, 7, 7, 7, 7, 7, 1] 90 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 36, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 178 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237515 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237515 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237515/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237515 Building REAL300000237516 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237516' /scratch/stefan/7769818/working/building/REAL300000237516 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237516 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237516/0 /scratch/stefan/7769818/working/building/REAL300000237516 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/516 `/scratch/stefan/7769818/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1) `REAL300000237516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237516 none O=C([O-])CCOC1=CC=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 75, 28, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 101, 101, 75, 75, 7, 7, 7, 1, 1, 1, 1, 1, 7] 101 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 365 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237516 none O=C([O-])CCOC1=CC=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [47, 37, 42, 28, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 37, 37, 28, 28, 1, 1, 1, 7, 7, 7, 7, 7, 1] 101 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 23, 28, 29, 30] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 182 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237516 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237516 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237516/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237516 Building REAL300000237517 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237517' /scratch/stefan/7769818/working/building/REAL300000237517 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237517 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237517/0 /scratch/stefan/7769818/working/building/REAL300000237517 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/517 `/scratch/stefan/7769818/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)O2)C=C1) `REAL300000237517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237517 none O=C([O-])C1=CC=C(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 12, 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, 7, 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 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 5, 5] 13 rigid atoms, others: [6, 7, 8, 9, 10, 11, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237517 none O=C([O-])C1=CC=C(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 12, 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, 7, 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 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 13, 13, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 13, 13] 13 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 42 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: REAL300000237517 none O=C([O-])C1=CC=C(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 12, 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, 7, 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 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, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 13, 1, 1] 13 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 24, 25, 26, 27, 36] 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]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237517 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237517 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237517/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237517 Building REAL300000237518 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237518' /scratch/stefan/7769818/working/building/REAL300000237518 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237518 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237518/0 /scratch/stefan/7769818/working/building/REAL300000237518 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/518 `/scratch/stefan/7769818/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1) `REAL300000237518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237518 none O=C([O-])COC1=CC=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 21, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 61, 61, 7, 7, 7, 1, 1, 1, 1, 1, 7] 61 rigid atoms, others: [32, 9, 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, 33, 22, 23, 24, 25, 26, 27]) total number of confs: 202 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237518 none O=C([O-])COC1=CC=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [32, 24, 32, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 24, 24, 1, 1, 1, 7, 7, 7, 7, 7, 1] 61 rigid atoms, others: [33, 4, 5, 6, 7, 8, 9, 10, 22, 25, 26, 27] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 28, 29, 30, 31, 32]) total number of confs: 119 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237518 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237518 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237518/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237518 Building REAL300000237519 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237519' /scratch/stefan/7769818/working/building/REAL300000237519 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237519 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237519/0 /scratch/stefan/7769818/working/building/REAL300000237519 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/519 `/scratch/stefan/7769818/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(COC2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C=C2)OC=C1) `REAL300000237519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237519 none O=C([O-])C1=C(COC2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C=C2)OC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 15, 11, 6, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 11, 11, 6, 6, 1, 1, 5, 5, 5, 5, 5, 1, 1, 11, 11] 27 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 23, 24, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 52 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237519 none O=C([O-])C1=C(COC2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C=C2)OC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 2, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 27, 27, 27, 16, 16, 5, 5, 1, 1, 1, 1, 1, 5, 5, 27, 27] 27 rigid atoms, others: [32, 33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40]) total number of confs: 80 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: REAL300000237519 none O=C([O-])C1=C(COC2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C=C2)OC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 10, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 1, 1, 1, 5, 5, 12, 12, 27, 27, 27, 27, 27, 11, 11, 1, 1] 27 rigid atoms, others: [1, 3, 4, 5, 39, 40, 25, 26, 27] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237519 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237519 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237519/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237519 Building REAL300000237520 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237520' /scratch/stefan/7769818/working/building/REAL300000237520 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237520 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237520/0 /scratch/stefan/7769818/working/building/REAL300000237520 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/520 `/scratch/stefan/7769818/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1) `REAL300000237520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237520 none O=C([O-])C(F)(F)OC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 22, 52, 52, 3, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7] 52 rigid atoms, others: [10, 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, 33, 32, 23, 24, 25, 26]) total number of confs: 173 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237520 none O=C([O-])C(F)(F)OC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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: [38, 28, 38, 7, 28, 28, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1] 52 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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 /scratch/stefan/7769818/working/building/REAL300000237520 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237520 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237520/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237520 Building REAL300000237521 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237521' /scratch/stefan/7769818/working/building/REAL300000237521 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237521 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237521/0 /scratch/stefan/7769818/working/building/REAL300000237521 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/521 `/scratch/stefan/7769818/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1) `REAL300000237521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237521 none COC1=C2OC(C(=O)[O-])=CC2=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6] 6 rigid atoms, others: [32, 33, 34, 11, 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, 35, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 7 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237521 none COC1=C2OC(C(=O)[O-])=CC2=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 2, 2, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 3, 3, 3, 1, 6, 6, 6, 6, 6, 1, 1] 6 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 35, 24, 25, 29, 36] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237521 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237521 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237521/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237521 Building REAL300000237522 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237522' /scratch/stefan/7769818/working/building/REAL300000237522 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237522 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237522/0 /scratch/stefan/7769818/working/building/REAL300000237522 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/522 `/scratch/stefan/7769818/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=C2CC3=NC(Cl)=CC=C3C2=O)N=N1) `REAL300000237522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237522 none O=C([O-])CN1C=C(C=C2CC3=NC(Cl)=CC=C3C2=O)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 17, 17, 8, 1, 1, 1, 1, 1] 17 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23]) total number of confs: 54 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237522 none O=C([O-])CN1C=C(C=C2CC3=NC(Cl)=CC=C3C2=O)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 9, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 8, 8, 8, 8] 17 rigid atoms, others: [3, 4, 5, 6, 7, 19, 20, 23] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237522 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237522 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237522/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237522 Building REAL300000237523 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237523' /scratch/stefan/7769818/working/building/REAL300000237523 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237523 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237523/0 /scratch/stefan/7769818/working/building/REAL300000237523 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/523 `/scratch/stefan/7769818/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1) `REAL300000237523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237523 none O=C([O-])C1=CSC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 3] 3 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 19, 20, 26]) total number of confs: 4 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237523 none O=C([O-])C1=CSC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3, 3, 3, 3, 1] 3 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237523 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237523 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237523/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237523 Building REAL300000237524 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237524' /scratch/stefan/7769818/working/building/REAL300000237524 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237524 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237524/0 /scratch/stefan/7769818/working/building/REAL300000237524 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/524 `/scratch/stefan/7769818/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1OCCC(=O)[O-]) `REAL300000237524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237524 none COC1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 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: [13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 36, 79, 97, 99, 99, 13, 13, 13, 5, 1, 1, 1, 1, 1, 5, 5, 79, 79, 97, 97] 99 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40]) total number of confs: 355 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237524 none COC1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 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: [3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 38, 53, 70, 70, 3, 3, 3, 1, 5, 5, 5, 5, 5, 1, 1, 38, 38, 53, 53] 99 rigid atoms, others: [1, 2, 3, 4, 5, 35, 17, 18, 19, 20, 36, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237524 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237524 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237524/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237524 Building REAL300000237525 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237525' /scratch/stefan/7769818/working/building/REAL300000237525 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237525 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237525/0 /scratch/stefan/7769818/working/building/REAL300000237525 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/525 `/scratch/stefan/7769818/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C(Cl)=C1) `REAL300000237525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237525 none O=C([O-])C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3] 3 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 29]) total number of confs: 9 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237525 none O=C([O-])C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1] 3 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237525 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237525 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237525/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237525 Building REAL300000237526 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237526' /scratch/stefan/7769818/working/building/REAL300000237526 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237526 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237526/0 /scratch/stefan/7769818/working/building/REAL300000237526 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/526 `/scratch/stefan/7769818/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)C(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1) `REAL300000237526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237526 none O=C([O-])C1=C(Cl)C(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5] 5 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 27, 28, 29]) total number of confs: 6 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237526 none O=C([O-])C1=C(Cl)C(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1] 5 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237526 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237526 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237526/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237526 Building REAL300000237527 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237527' /scratch/stefan/7769818/working/building/REAL300000237527 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237527 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237527/0 /scratch/stefan/7769818/working/building/REAL300000237527 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/527 `/scratch/stefan/7769818/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1O) `REAL300000237527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237527 none O=C([O-])C1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 12] 12 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 18, 19, 20, 21, 22, 28, 29, 30]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237527 none O=C([O-])C1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 1, 3, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 2] 12 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 30]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237527 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237527 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237527/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237527 Building REAL300000237528 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237528' /scratch/stefan/7769818/working/building/REAL300000237528 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237528 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237528/0 /scratch/stefan/7769818/working/building/REAL300000237528 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/528 `/scratch/stefan/7769818/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=C1CC2=NC(Cl)=CC=C2C1=O) `REAL300000237528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237528 none CC1=CC(C)=C(C(=O)[O-])C=C1C=C1CC2=NC(Cl)=CC=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 3 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 4 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237528 none CC1=CC(C)=C(C(=O)[O-])C=C1C=C1CC2=NC(Cl)=CC=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 2, 2, 2, 1, 3, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 26, 30] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237528 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237528 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237528/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237528 Building REAL300000237529 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237529' /scratch/stefan/7769818/working/building/REAL300000237529 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237529 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237529/0 /scratch/stefan/7769818/working/building/REAL300000237529 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/529 `/scratch/stefan/7769818/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1)C(=O)[O-]) `REAL300000237529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237529 none CC(OC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 22, 2, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 30, 30, 7, 7, 1, 1, 1, 1, 1, 7, 7] 30 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 84 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237529 none CC(OC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 16, 20, 20, 16, 16, 16, 16, 1, 1, 7, 7, 7, 7, 7, 1, 1] 30 rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 19, 20, 36, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 80 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237529 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237529 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237529/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237529 Building REAL300000237530 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237530' /scratch/stefan/7769818/working/building/REAL300000237530 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237530 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237530/0 /scratch/stefan/7769818/working/building/REAL300000237530 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/530 `/scratch/stefan/7769818/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC=C1C=C1CC2=NC(Cl)=CC=C2C1=O) `REAL300000237530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237530 none O=C([O-])CCOC1=CC=CC=C1C=C1CC2=NC(Cl)=CC=C2C1=O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 115, 96, 38, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 118, 118, 96, 96, 6, 6, 6, 6, 1, 1, 1, 1, 1] 118 rigid atoms, others: [32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 436 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237530 none O=C([O-])CCOC1=CC=CC=C1C=C1CC2=NC(Cl)=CC=C2C1=O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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: [86, 67, 83, 44, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 67, 67, 44, 44, 1, 1, 1, 1, 6, 6, 6, 6, 6] 118 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) total number of confs: 340 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237530 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237530 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237530/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237530 Building REAL300000237531 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237531' /scratch/stefan/7769818/working/building/REAL300000237531 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237531 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237531/0 /scratch/stefan/7769818/working/building/REAL300000237531 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/531 `/scratch/stefan/7769818/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)[O-])=C1C=C1CC2=NC(Cl)=CC=C2C1=O) `REAL300000237531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237531 none CN1N=CC(C(=O)[O-])=C1C=C1CC2=NC(Cl)=CC=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 1, 1, 1] 3 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24]) total number of confs: 4 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237531 none CN1N=CC(C(=O)[O-])=C1C=C1CC2=NC(Cl)=CC=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 3, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 24] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237531 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237531 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237531/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237531 Building REAL300000237532 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237532' /scratch/stefan/7769818/working/building/REAL300000237532 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237532 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237532/0 /scratch/stefan/7769818/working/building/REAL300000237532 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/532 `/scratch/stefan/7769818/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1F) `REAL300000237532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237532 none O=C([O-])C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3] 3 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 29]) total number of confs: 4 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237532 none O=C([O-])C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1] 3 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237532 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237532 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237532/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237532 Building REAL300000237533 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237533' /scratch/stefan/7769818/working/building/REAL300000237533 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237533 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237533/0 /scratch/stefan/7769818/working/building/REAL300000237533 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/533 `/scratch/stefan/7769818/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)O1) `REAL300000237533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237533 none O=C([O-])C=CC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 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, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 20, 20, 8, 8, 1, 1, 1, 1, 1] 20 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237533 none O=C([O-])C=CC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 14, 9, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 9, 9, 1, 1, 8, 8, 8, 8, 8] 20 rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237533 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237533 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237533/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237533 Building REAL300000237534 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237534' /scratch/stefan/7769818/working/building/REAL300000237534 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237534 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237534/0 /scratch/stefan/7769818/working/building/REAL300000237534 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/534 `/scratch/stefan/7769818/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1C(=O)[O-]) `REAL300000237534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237534 none COC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 12, 12, 12, 7, 7, 1, 1, 1, 1, 1, 7] 12 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 33, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237534 none COC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 7, 7, 7, 7, 7, 1] 12 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 18, 19, 20, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237534 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237534 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237534/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237534 Building REAL300000237535 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237535' /scratch/stefan/7769818/working/building/REAL300000237535 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237535 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237535/0 /scratch/stefan/7769818/working/building/REAL300000237535 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/535 `/scratch/stefan/7769818/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(F)C(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1) `REAL300000237535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237535 none O=C([O-])C1=CC=C(F)C(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 4] 4 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 29]) total number of confs: 5 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237535 none O=C([O-])C1=CC=C(F)C(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 1] 4 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237535 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237535 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237535/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237535 Building REAL300000237536 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237536' /scratch/stefan/7769818/working/building/REAL300000237536 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237536 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237536/0 /scratch/stefan/7769818/working/building/REAL300000237536 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/536 `/scratch/stefan/7769818/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C(=O)[O-])C=C1C=C1CC2=NC(Cl)=CC=C2C1=O) `REAL300000237536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237536 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=C1CC2=NC(Cl)=CC=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 7, 7, 7, 7, 12, 7, 7, 12, 12, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 7, 12, 12, 12, 7, 1, 1, 1, 1, 1] 20 rigid atoms, others: [33, 34, 35, 36, 37, 12, 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, 32, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237536 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=C1CC2=NC(Cl)=CC=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 1, 1, 3, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 1, 3, 3, 3, 1, 7, 7, 7, 7, 7] 20 rigid atoms, others: [32, 1, 2, 3, 4, 5, 7, 8, 11, 12, 13, 28] set([0, 6, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237536 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237536 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237536/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237536 Building REAL300000237537 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237537' /scratch/stefan/7769818/working/building/REAL300000237537 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237537 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237537/0 /scratch/stefan/7769818/working/building/REAL300000237537 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/537 `/scratch/stefan/7769818/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1F) `REAL300000237537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237537 none O=C([O-])C1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7] 7 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 18, 19, 20, 21, 22, 28, 29]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237537 none O=C([O-])C1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237537 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237537 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237537/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237537 Building REAL300000237538 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237538' /scratch/stefan/7769818/working/building/REAL300000237538 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237538 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237538/0 /scratch/stefan/7769818/working/building/REAL300000237538 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/538 `/scratch/stefan/7769818/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1) `REAL300000237538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237538 none O=C([O-])CC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=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', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 9 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237538 none O=C([O-])CC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=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', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1] 3 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237538 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237538 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237538/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237538 Building REAL300000237539 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237539' /scratch/stefan/7769818/working/building/REAL300000237539 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237539 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237539/0 /scratch/stefan/7769818/working/building/REAL300000237539 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/539 `/scratch/stefan/7769818/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(Br)=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1) `REAL300000237539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237539 none O=C([O-])C1=CC(Br)=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 4] 4 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 29]) total number of confs: 5 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237539 none O=C([O-])C1=CC(Br)=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 1] 4 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28]) total number of confs: 9 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237539 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237539 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237539/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237539 Building REAL300000237540 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237540' /scratch/stefan/7769818/working/building/REAL300000237540 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237540 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237540/0 /scratch/stefan/7769818/working/building/REAL300000237540 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/540 `/scratch/stefan/7769818/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)S1) `REAL300000237540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237540 none O=C([O-])C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1] 4 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 19, 20, 21]) total number of confs: 5 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237540 none O=C([O-])C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4] 4 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237540 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237540 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237540/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237540 Building REAL300000237541 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237541' /scratch/stefan/7769818/working/building/REAL300000237541 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237541 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237541/0 /scratch/stefan/7769818/working/building/REAL300000237541 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/541 `/scratch/stefan/7769818/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1) `REAL300000237541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237541 none O=C([O-])C=CC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 6, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7] 7 rigid atoms, others: [8, 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, 32, 33, 21, 22, 23, 24, 25, 26]) total number of confs: 27 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237541 none O=C([O-])C=CC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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: [5, 3, 5, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 3, 3, 1, 1, 7, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 21, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 29 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237541 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237541 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237541/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237541 Building REAL300000237542 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237542' /scratch/stefan/7769818/working/building/REAL300000237542 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237542 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237542/0 /scratch/stefan/7769818/working/building/REAL300000237542 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/542 `/scratch/stefan/7769818/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1F) `REAL300000237542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237542 none O=C([O-])C1=CC(F)=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7] 7 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 29]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237542 none O=C([O-])C1=CC(F)=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1] 7 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237542 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237542 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237542/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237542 Building REAL300000237543 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237543' /scratch/stefan/7769818/working/building/REAL300000237543 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237543 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237543/0 /scratch/stefan/7769818/working/building/REAL300000237543 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/543 `/scratch/stefan/7769818/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NNC2=CC=CC(C=C3CC4=NC(Cl)=CC=C4C3=O)=C21) `REAL300000237543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237543 none O=C([O-])C1=NNC2=CC=CC(C=C3CC4=NC(Cl)=CC=C4C3=O)=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1] 6 rigid atoms, others: [32, 10, 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, 23, 24, 25, 26, 27]) total number of confs: 7 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237543 none O=C([O-])C1=NNC2=CC=CC(C=C3CC4=NC(Cl)=CC=C4C3=O)=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 6 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27] set([0, 32, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237543 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237543 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237543/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237543 Building REAL300000237544 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237544' /scratch/stefan/7769818/working/building/REAL300000237544 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237544 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237544/0 /scratch/stefan/7769818/working/building/REAL300000237544 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/544 `/scratch/stefan/7769818/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C(C2=CC=CC=C2)=N1) `REAL300000237544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237544 none O=C([O-])CN1C=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [28, 25, 28, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 7, 19, 19, 7, 25, 25, 7, 1, 1, 1, 1, 1, 19, 19, 7, 19, 19] 32 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39]) total number of confs: 128 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237544 none O=C([O-])CN1C=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [22, 19, 22, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 6, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1] 32 rigid atoms, others: [35, 36, 37, 38, 39, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 107 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: REAL300000237544 none O=C([O-])CN1C=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 6, 6, 1, 6, 6, 1, 7, 7, 1, 7, 7, 7, 7, 7, 6, 6, 1, 6, 6] 32 rigid atoms, others: [3, 4, 5, 6, 7, 19, 20, 26, 29] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 27, 28, 30, 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 /scratch/stefan/7769818/working/building/REAL300000237544 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237544 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237544/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237544 Building REAL300000237545 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237545' /scratch/stefan/7769818/working/building/REAL300000237545 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237545 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237545/0 /scratch/stefan/7769818/working/building/REAL300000237545 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/545 `/scratch/stefan/7769818/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)O2)C=C1O) `REAL300000237545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237545 none O=C([O-])C1=CC=C(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)O2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [15, 9, 15, 9, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 9, 9, 9, 9, 9, 1, 1, 9, 9, 9, 9, 9, 9, 18] 84 rigid atoms, others: [6, 7, 8, 9, 10, 11, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237545 none O=C([O-])C1=CC=C(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)O2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [42, 42, 42, 42, 42, 42, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 42, 42, 42, 42, 42, 9, 9, 1, 1, 1, 1, 1, 42, 84] 84 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 37, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 134 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: REAL300000237545 none O=C([O-])C1=CC=C(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)O2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 3, 1, 1, 1, 1, 1, 9, 9, 9, 9, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 9, 1, 1, 1, 1, 1, 9, 9, 42, 42, 42, 42, 42, 1, 2] 84 rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26, 27, 28, 36] 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, 37]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237545 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237545 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237545/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237545 Building REAL300000237546 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237546' /scratch/stefan/7769818/working/building/REAL300000237546 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237546 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237546/0 /scratch/stefan/7769818/working/building/REAL300000237546 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/546 `/scratch/stefan/7769818/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C=C2)C=C1) `REAL300000237546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237546 none O=C([O-])C1=CC=C(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 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 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, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 3, 3, 3, 3, 1, 1, 2, 2, 2, 2, 2, 1, 1, 3, 3] 3 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 15 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237546 none O=C([O-])C1=CC=C(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 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 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, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 2, 2, 3, 3] 3 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39]) total number of confs: 10 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: REAL300000237546 none O=C([O-])C1=CC=C(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 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 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1] 3 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 15 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237546 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237546 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237546/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237546 Building REAL300000237547 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237547' /scratch/stefan/7769818/working/building/REAL300000237547 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237547 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237547/0 /scratch/stefan/7769818/working/building/REAL300000237547 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/547 `/scratch/stefan/7769818/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2NC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C2=C1) `REAL300000237547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237547 none O=C([O-])C1=CC=C2NC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7] 7 rigid atoms, others: [32, 9, 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, 33, 22, 23, 24, 25, 26, 27]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237547 none O=C([O-])C1=CC=C2NC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 22, 23, 24, 25, 26, 27] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237547 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237547 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237547/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237547 Building REAL300000237548 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237548' /scratch/stefan/7769818/working/building/REAL300000237548 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237548 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237548/0 /scratch/stefan/7769818/working/building/REAL300000237548 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/548 `/scratch/stefan/7769818/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=N1) `REAL300000237548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237548 none O=C([O-])C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3] 3 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 28]) total number of confs: 4 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237548 none O=C([O-])C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1] 3 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237548 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237548 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237548/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237548 Building REAL300000237549 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237549' /scratch/stefan/7769818/working/building/REAL300000237549 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237549 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237549/0 /scratch/stefan/7769818/working/building/REAL300000237549 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/549 `/scratch/stefan/7769818/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1O) `REAL300000237549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237549 none O=C([O-])C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 6] 6 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 29, 30]) total number of confs: 10 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237549 none O=C([O-])C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 2] 6 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 30]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237549 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237549 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237549/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237549 Building REAL300000237550 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237550' /scratch/stefan/7769818/working/building/REAL300000237550 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237550 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237550/0 /scratch/stefan/7769818/working/building/REAL300000237550 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/550 `/scratch/stefan/7769818/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1C(=O)[O-]) `REAL300000237550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237550 none CC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7] 7 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 32, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237550 none CC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 7, 7, 7, 7, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 17, 18, 19, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237550 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237550 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237550/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237550 Building REAL300000237551 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237551' /scratch/stefan/7769818/working/building/REAL300000237551 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237551 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237551/0 /scratch/stefan/7769818/working/building/REAL300000237551 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/551 `/scratch/stefan/7769818/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)SC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1) `REAL300000237551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237551 none O=C([O-])C1=C(Cl)SC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 1, 1, 1, 1, 1, 7] 7 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 20, 26]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237551 none O=C([O-])C1=C(Cl)SC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 1] 7 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237551 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237551 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237551/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237551 Building REAL300000237552 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237552' /scratch/stefan/7769818/working/building/REAL300000237552 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237552 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237552/0 /scratch/stefan/7769818/working/building/REAL300000237552 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/552 `/scratch/stefan/7769818/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=C2CC3=NC(Cl)=CC=C3C2=O)O1) `REAL300000237552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237552 none CC1=C(C(=O)[O-])C=C(C=C2CC3=NC(Cl)=CC=C3C2=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 12, 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, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1] 9 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24]) total number of confs: 10 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237552 none CC1=C(C(=O)[O-])C=C(C=C2CC3=NC(Cl)=CC=C3C2=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 12, 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, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 1, 9, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 20, 24] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237552 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237552 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237552/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237552 Building REAL300000237553 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237553' /scratch/stefan/7769818/working/building/REAL300000237553 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237553 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237553/0 /scratch/stefan/7769818/working/building/REAL300000237553 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/553 `/scratch/stefan/7769818/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)S2)C=C1) `REAL300000237553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237553 none O=C([O-])C1=CC=C(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 4, 4, 4, 4, 1, 1, 5, 5, 5, 5, 5, 4, 4] 8 rigid atoms, others: [6, 7, 8, 9, 10, 11, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 30 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237553 none O=C([O-])C1=CC=C(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 5, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 8, 8] 8 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 28 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: REAL300000237553 none O=C([O-])C1=CC=C(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 1, 1] 8 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 24, 25, 26, 27, 36] 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]) total number of confs: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237553 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237553 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237553/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237553 Building REAL300000237554 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237554' /scratch/stefan/7769818/working/building/REAL300000237554 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237554 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237554/0 /scratch/stefan/7769818/working/building/REAL300000237554 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/554 `/scratch/stefan/7769818/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=C1CC2=NC(Cl)=CC=C2C1=O) `REAL300000237554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237554 none CN1N=C(C(=O)[O-])C=C1C=C1CC2=NC(Cl)=CC=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 1, 1, 1] 3 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24]) total number of confs: 4 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237554 none CN1N=C(C(=O)[O-])C=C1C=C1CC2=NC(Cl)=CC=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 3, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237554 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237554 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237554/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237554 Building REAL300000237555 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237555' /scratch/stefan/7769818/working/building/REAL300000237555 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237555 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237555/0 /scratch/stefan/7769818/working/building/REAL300000237555 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/555 `/scratch/stefan/7769818/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)O2)=CC=C1O) `REAL300000237555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237555 none O=C([O-])C1=CC(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [18, 13, 18, 13, 13, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 13, 13, 12, 12, 13, 1, 1, 8, 8, 8, 8, 8, 13, 13, 26] 128 rigid atoms, others: [5, 6, 7, 8, 9, 10, 22, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237555 none O=C([O-])C1=CC(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [64, 64, 64, 64, 64, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 64, 64, 64, 64, 64, 8, 8, 1, 1, 1, 1, 1, 64, 64, 128] 128 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 37, 35, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 200 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237555 none O=C([O-])C1=CC(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 13, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 13, 1, 1, 1, 1, 1, 13, 13, 64, 64, 64, 64, 64, 1, 1, 2] 128 rigid atoms, others: [1, 3, 4, 5, 6, 35, 23, 24, 25, 26, 27, 36] 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, 37]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237555 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237555 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237555/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237555 Building REAL300000237556 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237556' /scratch/stefan/7769818/working/building/REAL300000237556 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237556 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237556/0 /scratch/stefan/7769818/working/building/REAL300000237556 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/556 `/scratch/stefan/7769818/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1) `REAL300000237556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237556 none O=C([O-])C1=CN=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 4] 4 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 28]) total number of confs: 5 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237556 none O=C([O-])C1=CN=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 1] 4 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237556 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237556 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237556/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237556 Building REAL300000237557 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237557' /scratch/stefan/7769818/working/building/REAL300000237557 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237557 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237557/0 /scratch/stefan/7769818/working/building/REAL300000237557 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/557 `/scratch/stefan/7769818/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)S2)=C1) `REAL300000237557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237557 none O=C([O-])C1=CC=CC(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 14, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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: [12, 11, 12, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 11, 11, 11, 11, 1, 1, 7, 7, 7, 7, 7, 11] 18 rigid atoms, others: [7, 8, 9, 10, 11, 12, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 30 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237557 none O=C([O-])C1=CC=CC(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 14, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18, 7, 7, 1, 1, 1, 1, 1, 18] 18 rigid atoms, others: [32, 33, 34, 35, 11, 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, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 23 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: REAL300000237557 none O=C([O-])C1=CC=CC(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 14, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 1, 1, 1, 1, 11, 11, 18, 18, 18, 18, 18, 1] 18 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 36] 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: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237557 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237557 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237557/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237557 Building REAL300000237558 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237558' /scratch/stefan/7769818/working/building/REAL300000237558 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237558 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237558/0 /scratch/stefan/7769818/working/building/REAL300000237558 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/558 `/scratch/stefan/7769818/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=C1CC2=NC(Cl)=CC=C2C1=O) `REAL300000237558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237558 none COC1=CC=C(C(=O)[O-])C=C1C=C1CC2=NC(Cl)=CC=C2C1=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', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1] 7 rigid atoms, others: [32, 33, 10, 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, 23, 24, 25, 26, 27, 28]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237558 none COC1=CC=C(C(=O)[O-])C=C1C=C1CC2=NC(Cl)=CC=C2C1=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', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 1, 1, 1, 7, 7, 7, 7, 7] 7 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237558 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237558 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237558/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237558 Building REAL300000237559 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237559' /scratch/stefan/7769818/working/building/REAL300000237559 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237559 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237559/0 /scratch/stefan/7769818/working/building/REAL300000237559 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/559 `/scratch/stefan/7769818/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2SC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C2=C1) `REAL300000237559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237559 none O=C([O-])C1=CC=C2SC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6] 6 rigid atoms, others: [9, 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, 32, 22, 23, 24, 25, 26]) total number of confs: 7 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237559 none O=C([O-])C1=CC=C2SC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1] 6 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237559 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237559 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237559/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237559 Building REAL300000237560 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237560' /scratch/stefan/7769818/working/building/REAL300000237560 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237560 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237560/0 /scratch/stefan/7769818/working/building/REAL300000237560 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/560 `/scratch/stefan/7769818/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Br)C(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1) `REAL300000237560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237560 none O=C([O-])C1=CC=C(Br)C(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 3] 3 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 29]) total number of confs: 4 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237560 none O=C([O-])C1=CC=C(Br)C(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 1] 3 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237560 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237560 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237560/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237560 Building REAL300000237561 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237561' /scratch/stefan/7769818/working/building/REAL300000237561 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237561 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237561/0 /scratch/stefan/7769818/working/building/REAL300000237561 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/561 `/scratch/stefan/7769818/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C([N+](=O)[O-])=C1) `REAL300000237561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237561 none O=C([O-])C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3] 3 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 4 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237561 none O=C([O-])C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 1] 3 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237561 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237561 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237561/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237561 Building REAL300000237562 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237562' /scratch/stefan/7769818/working/building/REAL300000237562 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237562 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237562/0 /scratch/stefan/7769818/working/building/REAL300000237562 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/562 `/scratch/stefan/7769818/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1) `REAL300000237562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237562 none O=C([O-])CC1=CC=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 7, 7, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 6, 7, 7, 1, 1, 1, 1, 1, 7] 11 rigid atoms, others: [8, 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, 32, 21, 22, 23, 24, 25, 26]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237562 none O=C([O-])CC1=CC=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 2, 2, 1, 1, 1, 7, 7, 7, 7, 7, 1] 11 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 21, 24, 25, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237562 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237562 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237562/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237562 Building REAL300000237563 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237563' /scratch/stefan/7769818/working/building/REAL300000237563 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237563 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237563/0 /scratch/stefan/7769818/working/building/REAL300000237563 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/563 `/scratch/stefan/7769818/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1C(=O)[O-]) `REAL300000237563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237563 none COC1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 1, 1, 1, 1, 1, 7, 7] 9 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 33, 32, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 20 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237563 none COC1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 7, 7, 7, 7, 7, 1, 1] 9 rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 17, 18, 19, 20, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237563 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237563 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237563/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237563 Building REAL300000237564 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237564' /scratch/stefan/7769818/working/building/REAL300000237564 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237564 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237564/0 /scratch/stefan/7769818/working/building/REAL300000237564 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/564 `/scratch/stefan/7769818/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C(F)=C1) `REAL300000237564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237564 none O=C([O-])C1=CC(F)=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2] 2 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 29]) total number of confs: 10 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237564 none O=C([O-])C1=CC(F)=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1] 2 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 9 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237564 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237564 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237564/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237564 Building REAL300000237565 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237565' /scratch/stefan/7769818/working/building/REAL300000237565 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237565 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237565/0 /scratch/stefan/7769818/working/building/REAL300000237565 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/565 `/scratch/stefan/7769818/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C(C=C2CC3=NC(Cl)=CC=C3C2=O)=C(F)C=C1) `REAL300000237565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237565 none O=C([O-])C1=C(F)C(C=C2CC3=NC(Cl)=CC=C3C2=O)=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7] 7 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 28, 29]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237565 none O=C([O-])C1=C(F)C(C=C2CC3=NC(Cl)=CC=C3C2=O)=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237565 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237565 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237565/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237565 Building REAL300000237566 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237566' /scratch/stefan/7769818/working/building/REAL300000237566 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237566 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237566/0 /scratch/stefan/7769818/working/building/REAL300000237566 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/566 `/scratch/stefan/7769818/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C=C2)=C1) `REAL300000237566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237566 none O=C([O-])CC1=CC=CC(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 7, 7, 7, 7, 7, 1, 1, 3] 15 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 40, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 42]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237566 none O=C([O-])CC1=CC=CC(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 9, 9, 2, 9, 9, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 15, 15, 4, 9, 9, 7, 7, 1, 1, 1, 1, 1, 7, 7, 9] 15 rigid atoms, others: [35, 36, 37, 38, 39, 12, 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, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 73 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: REAL300000237566 none O=C([O-])CC1=CC=CC(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 3, 3, 1] 15 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 42, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237566 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237566 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237566/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237566 Building REAL300000237567 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237567' /scratch/stefan/7769818/working/building/REAL300000237567 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237567 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237567/0 /scratch/stefan/7769818/working/building/REAL300000237567 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/567 `/scratch/stefan/7769818/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CS1) `REAL300000237567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237567 none O=C([O-])C1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 4] 4 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 18, 19, 20, 26]) total number of confs: 5 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237567 none O=C([O-])C1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 1] 4 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237567 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237567 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237567/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237567 Building REAL300000237568 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237568' /scratch/stefan/7769818/working/building/REAL300000237568 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237568 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237568/0 /scratch/stefan/7769818/working/building/REAL300000237568 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/568 `/scratch/stefan/7769818/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1OCC(=O)[O-]) `REAL300000237568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237568 none CCOC1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 36, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 45, 131, 168, 168, 102, 102, 102, 102, 102, 7, 1, 1, 1, 1, 1, 7, 7, 131, 131] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40]) total number of confs: 850 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237568 none CCOC1=CC(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 9, 41, 78, 78, 38, 38, 38, 38, 38, 1, 7, 7, 7, 7, 7, 1, 1, 41, 41] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 19, 20, 21, 38, 37, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237568 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237568 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237568/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237568 Building REAL300000237569 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237569' /scratch/stefan/7769818/working/building/REAL300000237569 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237569 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237569/0 /scratch/stefan/7769818/working/building/REAL300000237569 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/569 `/scratch/stefan/7769818/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1F) `REAL300000237569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237569 none O=C([O-])C1=C(F)C=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4] 4 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 29]) total number of confs: 10 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237569 none O=C([O-])C1=C(F)C=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1] 4 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237569 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237569 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237569/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237569 Building REAL300000237570 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237570' /scratch/stefan/7769818/working/building/REAL300000237570 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237570 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237570/0 /scratch/stefan/7769818/working/building/REAL300000237570 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/570 `/scratch/stefan/7769818/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=C(C=C3CC4=NC(Cl)=CC=C4C3=O)O2)N1) `REAL300000237570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237570 none O=C([O-])C1=CC2=C(C=C(C=C3CC4=NC(Cl)=CC=C4C3=O)O2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 4, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5] 5 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30]) total number of confs: 6 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237570 none O=C([O-])C1=CC2=C(C=C(C=C3CC4=NC(Cl)=CC=C4C3=O)O2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 4, 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, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237570 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237570 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237570/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237570 Building REAL300000237571 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237571' /scratch/stefan/7769818/working/building/REAL300000237571 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237571 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237571/0 /scratch/stefan/7769818/working/building/REAL300000237571 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/571 `/scratch/stefan/7769818/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC(C=C3CC4=NC(Cl)=CC=C4C3=O)=CC=C2O1) `REAL300000237571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237571 none O=C([O-])C1=CC2=CC(C=C3CC4=NC(Cl)=CC=C4C3=O)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 4 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237571 none O=C([O-])C1=CC2=CC(C=C3CC4=NC(Cl)=CC=C4C3=O)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1] 3 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237571 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237571 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237571/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237571 Building REAL300000237572 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237572' /scratch/stefan/7769818/working/building/REAL300000237572 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237572 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237572/0 /scratch/stefan/7769818/working/building/REAL300000237572 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/572 `/scratch/stefan/7769818/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2C(C=C3CC4=NC(Cl)=CC=C4C3=O)=CC=CN12) `REAL300000237572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237572 none O=C([O-])C1=CN=C2C(C=C3CC4=NC(Cl)=CC=C4C3=O)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3] 3 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 32, 20, 21, 22, 23, 24, 30, 31]) total number of confs: 4 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237572 none O=C([O-])C1=CN=C2C(C=C3CC4=NC(Cl)=CC=C4C3=O)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29]) total number of confs: 7 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237572 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237572 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237572/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237572 Building REAL300000237573 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237573' /scratch/stefan/7769818/working/building/REAL300000237573 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237573 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237573/0 /scratch/stefan/7769818/working/building/REAL300000237573 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/573 `/scratch/stefan/7769818/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=C1CC2=NC(Cl)=CC=C2C1=O) `REAL300000237573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237573 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=C1CC2=NC(Cl)=CC=C2C1=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', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1] 5 rigid atoms, others: [33, 34, 35, 36, 37, 13, 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, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 6 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237573 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=C1CC2=NC(Cl)=CC=C2C1=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', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 5] 5 rigid atoms, others: [0, 1, 2, 3, 32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([33, 34, 35, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 36]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237573 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237573 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237573/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237573 Building REAL300000237574 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237574' /scratch/stefan/7769818/working/building/REAL300000237574 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237574 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237574/0 /scratch/stefan/7769818/working/building/REAL300000237574 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/574 `/scratch/stefan/7769818/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN2C(C=C3CC4=NC(Cl)=CC=C4C3=O)=CN=C2C=C1) `REAL300000237574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237574 none O=C([O-])C1=CN2C(C=C3CC4=NC(Cl)=CC=C4C3=O)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 8, 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, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7] 7 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 24, 30, 31]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237574 none O=C([O-])C1=CN2C(C=C3CC4=NC(Cl)=CC=C4C3=O)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 8, 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, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1] 7 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237574 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237574 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237574/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237574 Building REAL300000237575 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237575' /scratch/stefan/7769818/working/building/REAL300000237575 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237575 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237575/0 /scratch/stefan/7769818/working/building/REAL300000237575 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/575 `/scratch/stefan/7769818/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C=C2)C=N1) `REAL300000237575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237575 none O=C([O-])C1=CN(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 4, 4, 4, 1, 1, 7, 7, 7, 7, 7, 1, 1, 4] 7 rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 36]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237575 none O=C([O-])C1=CN(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7] 7 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 22, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 25 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: REAL300000237575 none O=C([O-])C1=CN(C2=CC=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 4, 4, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25, 26, 36] set([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: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237575 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237575 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237575/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237575 Building REAL300000237576 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237576' /scratch/stefan/7769818/working/building/REAL300000237576 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237576 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237576/0 /scratch/stefan/7769818/working/building/REAL300000237576 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/576 `/scratch/stefan/7769818/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1) `REAL300000237576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237576 none O=C([O-])C1=C(F)C(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7] 7 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 27, 28, 29]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237576 none O=C([O-])C1=C(F)C(C=C2CC3=NC(Cl)=CC=C3C2=O)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1] 7 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237576 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237576 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237576/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237576 Building REAL300000237577 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237577' /scratch/stefan/7769818/working/building/REAL300000237577 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237577 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237577/0 /scratch/stefan/7769818/working/building/REAL300000237577 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/577 `/scratch/stefan/7769818/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1Cl) `REAL300000237577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237577 none O=C([O-])COC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 32, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 54, 54, 7, 7, 1, 1, 1, 1, 1, 7] 54 rigid atoms, others: [32, 8, 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, 33, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 152 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237577 none O=C([O-])COC1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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: [43, 35, 43, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 35, 35, 1, 1, 7, 7, 7, 7, 7, 1] 54 rigid atoms, others: [33, 4, 5, 6, 7, 8, 9, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237577 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237577 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237577/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237577 Building REAL300000237578 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237578' /scratch/stefan/7769818/working/building/REAL300000237578 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237578 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237578/0 /scratch/stefan/7769818/working/building/REAL300000237578 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/578 `/scratch/stefan/7769818/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNS(=O)(=O)C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1) `REAL300000237578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237578 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 20, 7, 1, 7, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 42, 42, 20, 7, 7, 1, 1, 1, 1, 1, 7, 7] 42 rigid atoms, others: [32, 33, 34, 35, 11, 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, 37, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237578 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [34, 27, 34, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 27, 27, 5, 1, 1, 7, 7, 7, 7, 7, 1, 1] 42 rigid atoms, others: [36, 5, 8, 9, 10, 11, 12, 24, 25, 29, 30, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237578 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237578 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237578/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237578 Building REAL300000237579 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237579' /scratch/stefan/7769818/working/building/REAL300000237579 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237579 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237579/0 /scratch/stefan/7769818/working/building/REAL300000237579 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/579 `/scratch/stefan/7769818/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC=C1C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1) `REAL300000237579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237579 none O=C([O-])C1=CC=CC=C1C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 4, 4, 3, 4, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 4, 3, 4, 4, 1, 1, 6, 6, 6, 6, 6, 1, 1] 7 rigid atoms, others: [32, 38, 39, 8, 9, 10, 11, 12, 13, 25, 26, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 24 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237579 none O=C([O-])C1=CC=CC=C1C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 7, 7, 1, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 6, 1, 1, 1, 1, 1, 6, 6] 7 rigid atoms, others: [33, 34, 35, 36, 37, 12, 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, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 26 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: REAL300000237579 none O=C([O-])C1=CC=CC=C1C1=CC=C(C=C2CC3=NC(Cl)=CC=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 4, 4] 7 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237579 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237579 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237579/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237579 Building REAL300000237580 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237580' /scratch/stefan/7769818/working/building/REAL300000237580 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237580 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237580/0 /scratch/stefan/7769818/working/building/REAL300000237580 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/580 `/scratch/stefan/7769818/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=C1CC2=NC(Cl)=CC=C2C1=O) `REAL300000237580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237580 none COC1=CC(C(=O)[O-])=CC=C1C=C1CC2=NC(Cl)=CC=C2C1=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', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1] 5 rigid atoms, others: [32, 33, 10, 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, 23, 24, 25, 26, 27, 28]) total number of confs: 6 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237580 none COC1=CC(C(=O)[O-])=CC=C1C=C1CC2=NC(Cl)=CC=C2C1=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', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5] 5 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237580 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237580 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237580/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237580 Building REAL300000237581 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237581' /scratch/stefan/7769818/working/building/REAL300000237581 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237581 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237581/0 /scratch/stefan/7769818/working/building/REAL300000237581 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/581 `/scratch/stefan/7769818/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C(F)=CC=C2S1) `REAL300000237581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237581 none O=C([O-])C1=CC2=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7] 7 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237581 none O=C([O-])C1=CC2=C(C=C3CC4=NC(Cl)=CC=C4C3=O)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237581 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237581 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237581/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237581 Building REAL300000237582 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237582' /scratch/stefan/7769818/working/building/REAL300000237582 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237582 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237582/0 /scratch/stefan/7769818/working/building/REAL300000237582 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/582 `/scratch/stefan/7769818/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=CC=C1OCC(=O)[O-]) `REAL300000237582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237582 none COC1=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 51, 128, 129, 129, 18, 18, 18, 7, 1, 1, 1, 1, 1, 1, 7, 7, 128, 128] 129 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 36, 37, 38, 39, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 409 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237582 none COC1=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 10, 51, 71, 71, 4, 4, 4, 1, 7, 7, 7, 7, 7, 7, 1, 1, 51, 51] 129 rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 20, 21, 36, 29, 37] set([0, 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, 38, 39]) total number of confs: 256 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237582 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237582 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237582/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237582 Building REAL300000237583 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237583' /scratch/stefan/7769818/working/building/REAL300000237583 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237583 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237583/0 /scratch/stefan/7769818/working/building/REAL300000237583 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/583 `/scratch/stefan/7769818/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(OCC(=O)[O-])C=C3)C(=O)C2=C1) `REAL300000237583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237583 none N#CC1=CC=C2CC(=CC3=CC=C(OCC(=O)[O-])C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 5, 19, 23, 23, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 20, 20, 1, 1, 4] 23 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35]) total number of confs: 88 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237583 none N#CC1=CC=C2CC(=CC3=CC=C(OCC(=O)[O-])C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 4, 4, 1, 2, 12, 23, 23, 23, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 23, 23, 4, 4, 1] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237583 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237583 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237583/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237583 Building REAL300000237584 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237584' /scratch/stefan/7769818/working/building/REAL300000237584 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237584 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237584/0 /scratch/stefan/7769818/working/building/REAL300000237584 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/584 `/scratch/stefan/7769818/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(OCCC(=O)[O-])C=C3)C(=O)C2=C1) `REAL300000237584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237584 none N#CC1=CC=C2CC(=CC3=CC=C(OCCC(=O)[O-])C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 6, 17, 26, 32, 29, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 17, 17, 25, 25, 1, 1, 4] 41 rigid atoms, others: [36, 37, 8, 9, 10, 11, 12, 13, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 38]) total number of confs: 124 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237584 none N#CC1=CC=C2CC(=CC3=CC=C(OCCC(=O)[O-])C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 4, 4, 1, 2, 14, 33, 41, 41, 39, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 33, 33, 41, 41, 4, 4, 1] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([32, 33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31]) total number of confs: 154 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237584 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237584 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237584/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237584 Building REAL300000237585 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237585' /scratch/stefan/7769818/working/building/REAL300000237585 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237585 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237585/0 /scratch/stefan/7769818/working/building/REAL300000237585 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/585 `/scratch/stefan/7769818/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=C1)C(=O)[O-]) `REAL300000237585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237585 none CC(OC1=CC=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 56, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 87, 87, 87, 87, 87, 87, 87, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7] 87 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 38, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 237 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237585 none CC(OC1=CC=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [35, 13, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 35, 39, 39, 35, 35, 35, 35, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1] 87 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 21, 38, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 140 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237585 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237585 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237585/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237585 Building REAL300000237586 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237586' /scratch/stefan/7769818/working/building/REAL300000237586 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237586 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237586/0 /scratch/stefan/7769818/working/building/REAL300000237586 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/586 `/scratch/stefan/7769818/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=CC(OCCC(=O)[O-])=C3)C(=O)C2=C1) `REAL300000237586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237586 none N#CC1=CC=C2CC(=CC3=CC=CC(OCCC(=O)[O-])=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 26, 35, 40, 37, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 26, 26, 35, 35, 1, 7] 95 rigid atoms, others: [32, 37, 8, 9, 10, 11, 12, 13, 14, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 38]) total number of confs: 158 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237586 none N#CC1=CC=C2CC(=CC3=CC=CC(OCCC(=O)[O-])=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 7, 7, 33, 73, 95, 95, 92, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 73, 73, 95, 95, 7, 1] 95 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([32, 33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31]) total number of confs: 346 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237586 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237586 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237586/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237586 Building REAL300000237587 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237587' /scratch/stefan/7769818/working/building/REAL300000237587 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237587 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237587/0 /scratch/stefan/7769818/working/building/REAL300000237587 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/587 `/scratch/stefan/7769818/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=CC(OCC4=CC=CC=C4C(=O)[O-])=C3)C(=O)C2=C1) `REAL300000237587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237587 none N#CC1=CC=C2CC(=CC3=CC=CC(OCC4=CC=CC=C4C(=O)[O-])=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 7, 17, 18, 18, 18, 18, 18, 18, 18, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7, 18, 18, 18, 18, 1, 7] 54 rigid atoms, others: [35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 45]) total number of confs: 52 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237587 none N#CC1=CC=C2CC(=CC3=CC=CC(OCC4=CC=CC=C4C(=O)[O-])=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 18, 17, 18, 18, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 18, 54, 54, 54, 54, 54, 54, 54, 54, 54, 17, 18, 18, 5, 5, 1, 1, 1, 1, 18, 54] 54 rigid atoms, others: [40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45]) total number of confs: 146 number of broken/clashed sets: 13 ./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: REAL300000237587 none N#CC1=CC=C2CC(=CC3=CC=CC(OCC4=CC=CC=C4C(=O)[O-])=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 13, 22, 54, 54, 54, 54, 54, 54, 54, 54, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 54, 54, 54, 54, 7, 1] 54 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 45, 26, 32, 33, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 106 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237587 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237587 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237587/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237587 Building REAL300000237588 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237588' /scratch/stefan/7769818/working/building/REAL300000237588 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237588 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237588/0 /scratch/stefan/7769818/working/building/REAL300000237588 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/588 `/scratch/stefan/7769818/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])OC(COC2=CC=C(C=C3CC4=CC=C(C#N)C=C4C3=O)C=C2)=C1) `REAL300000237588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237588 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=C3CC4=CC=C(C#N)C=C4C3=O)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.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, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 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, 2, 2, 3, 7, 7, 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, 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: [59, 59, 59, 59, 68, 68, 59, 14, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 59, 59, 59, 59, 14, 14, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 59] 116 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 44, 43, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 148 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237588 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=C3CC4=CC=C(C#N)C=C4C3=O)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.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, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 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, 2, 2, 3, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 116, 116, 116, 38, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 116, 116, 116, 116, 38, 38, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 116] 116 rigid atoms, others: [37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 229 number of broken/clashed sets: 55 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237588 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=C3CC4=CC=C(C#N)C=C4C3=O)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.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, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 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, 2, 2, 3, 7, 7, 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, 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, 2, 2, 1, 1, 1, 9, 42, 59, 59, 59, 59, 116, 116, 116, 116, 116, 116, 116, 116, 116, 116, 116, 116, 59, 59, 1, 2, 2, 2, 9, 9, 59, 59, 116, 116, 116, 116, 116, 116, 58, 59, 1] 116 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 45, 29] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 307 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237588 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237588 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237588/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237588 Building REAL300000237589 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237589' /scratch/stefan/7769818/working/building/REAL300000237589 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237589 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237589/0 /scratch/stefan/7769818/working/building/REAL300000237589 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/589 `/scratch/stefan/7769818/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)O3)C(=O)C2=C1) `REAL300000237589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237589 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)O3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 4, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 4, 4, 4, 4, 7] 19 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 32 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237589 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)O3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 1, 1, 1, 1, 19] 19 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 45 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: REAL300000237589 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)O3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 19, 19, 7, 7, 19, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237589 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237589 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237589/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237589 Building REAL300000237590 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237590' /scratch/stefan/7769818/working/building/REAL300000237590 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237590 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237590/0 /scratch/stefan/7769818/working/building/REAL300000237590 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/590 `/scratch/stefan/7769818/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=CC(OCC4=CC=CC(C(=O)[O-])=C4)=C3)C(=O)C2=C1) `REAL300000237590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237590 none N#CC1=CC=C2CC(=CC3=CC=CC(OCC4=CC=CC(C(=O)[O-])=C4)=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 4, 21, 67, 67, 67, 67, 67, 68, 68, 67, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 21, 21, 67, 67, 67, 67, 1, 7] 201 rigid atoms, others: [35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 45]) total number of confs: 147 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237590 none N#CC1=CC=C2CC(=CC3=CC=CC(OCC4=CC=CC(C(=O)[O-])=C4)=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 201, 201, 201, 201, 67, 67, 67, 67, 67, 36, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 67, 68, 67, 8, 8, 1, 1, 1, 1, 67, 201] 201 rigid atoms, others: [40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45]) total number of confs: 473 number of broken/clashed sets: 60 ./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: REAL300000237590 none N#CC1=CC=C2CC(=CC3=CC=CC(OCC4=CC=CC(C(=O)[O-])=C4)=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 21, 66, 201, 201, 201, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 66, 66, 201, 201, 201, 201, 7, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 45, 26, 32, 33, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 393 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237590 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237590 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237590/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237590 Building REAL300000237591 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237591' /scratch/stefan/7769818/working/building/REAL300000237591 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237591 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237591/0 /scratch/stefan/7769818/working/building/REAL300000237591 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/591 `/scratch/stefan/7769818/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=C([N+](=O)[O-])C=C1OCC(=O)[O-]) `REAL300000237591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237591 none COC1=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 36, 86, 89, 89, 12, 12, 12, 5, 1, 1, 1, 1, 1, 1, 5, 86, 86] 89 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 36, 38, 37] set([0, 1, 2, 3, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41]) total number of confs: 274 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237591 none COC1=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=C([N+](=O)[O-])C=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 1, 1, 1, 9, 34, 48, 48, 4, 4, 4, 1, 5, 5, 5, 5, 5, 5, 1, 34, 34] 89 rigid atoms, others: [32, 1, 2, 3, 4, 5, 39, 18, 19, 22, 23, 24] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 188 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237591 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237591 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237591/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237591 Building REAL300000237592 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237592' /scratch/stefan/7769818/working/building/REAL300000237592 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237592 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237592/0 /scratch/stefan/7769818/working/building/REAL300000237592 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/592 `/scratch/stefan/7769818/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=CC(OCC(=O)[O-])=C3)C(=O)C2=C1) `REAL300000237592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237592 none N#CC1=CC=C2CC(=CC3=CC=CC(OCC(=O)[O-])=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', '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, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 6, 26, 35, 35, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 26, 26, 1, 7] 68 rigid atoms, others: [34, 8, 9, 10, 11, 12, 13, 14, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 35]) total number of confs: 129 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237592 none N#CC1=CC=C2CC(=CC3=CC=CC(OCC(=O)[O-])=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', '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, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 26, 68, 68, 68, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 68, 68, 7, 1] 68 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 228 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237592 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237592 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237592/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237592 Building REAL300000237593 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237593' /scratch/stefan/7769818/working/building/REAL300000237593 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237593 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237593/0 /scratch/stefan/7769818/working/building/REAL300000237593 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/593 `/scratch/stefan/7769818/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(OCC4=C(C(=O)[O-])C=CO4)C=C3)C(=O)C2=C1) `REAL300000237593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237593 none N#CC1=CC=C2CC(=CC3=CC=C(OCC4=C(C(=O)[O-])C=CO4)C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 10, 20, 20, 21, 21, 20, 20, 20, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 10, 10, 20, 20, 1, 1, 3] 26 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 40, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 42]) total number of confs: 57 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237593 none N#CC1=CC=C2CC(=CC3=CC=C(OCC4=C(C(=O)[O-])C=CO4)C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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, 20, 20, 20, 20, 12, 6, 1, 1, 1, 1, 3, 3, 1, 1, 1, 20, 20, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 6, 6, 1, 1, 20, 20, 26] 26 rigid atoms, others: [38, 39, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 74 number of broken/clashed sets: 11 ./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: REAL300000237593 none N#CC1=CC=C2CC(=CC3=CC=C(OCC4=C(C(=O)[O-])C=CO4)C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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, 3, 3, 3, 3, 6, 16, 26, 26, 26, 26, 26, 26, 26, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 16, 16, 26, 26, 3, 3, 1] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 42, 26, 32, 25, 33, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237593 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237593 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237593/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237593 Building REAL300000237594 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237594' /scratch/stefan/7769818/working/building/REAL300000237594 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237594 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237594/0 /scratch/stefan/7769818/working/building/REAL300000237594 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/594 `/scratch/stefan/7769818/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(OC(F)(F)C(=O)[O-])C=C3)C(=O)C2=C1) `REAL300000237594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237594 none N#CC1=CC=C2CC(=CC3=CC=C(OC(F)(F)C(=O)[O-])C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 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, 7, 7, 3, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 12, 44, 44, 44, 53, 53, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4] 53 rigid atoms, others: [32, 33, 34, 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, 35]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237594 none N#CC1=CC=C2CC(=CC3=CC=C(OC(F)(F)C(=O)[O-])C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 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, 7, 7, 3, 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 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, 4, 4, 2, 2, 21, 53, 53, 53, 53, 53, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1] 53 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237594 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237594 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237594/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237594 Building REAL300000237595 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237595' /scratch/stefan/7769818/working/building/REAL300000237595 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237595 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237595/0 /scratch/stefan/7769818/working/building/REAL300000237595 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/595 `/scratch/stefan/7769818/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(OCC(=O)[O-])C(Br)=C3)C(=O)C2=C1) `REAL300000237595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237595 none N#CC1=CC=C2CC(=CC3=CC=C(OCC(=O)[O-])C(Br)=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', '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, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 1, 11, 1, 1, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 9, 34, 42, 42, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 34, 34, 1, 7] 52 rigid atoms, others: [34, 8, 9, 10, 11, 12, 13, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35]) total number of confs: 147 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237595 none N#CC1=CC=C2CC(=CC3=CC=C(OCC(=O)[O-])C(Br)=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', '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, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 1, 11, 1, 1, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 2, 2, 30, 52, 52, 52, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 52, 52, 7, 1] 52 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237595 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237595 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237595/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237595 Building REAL300000237596 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237596' /scratch/stefan/7769818/working/building/REAL300000237596 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237596 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237596/0 /scratch/stefan/7769818/working/building/REAL300000237596 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/596 `/scratch/stefan/7769818/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=C2CC3=CC=C(C#N)C=C3C2=O)C=C1) `REAL300000237596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237596 none COC1=C2OC(C(=O)[O-])=CC2=C(C=C2CC3=CC=C(C#N)C=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6] 6 rigid atoms, others: [32, 33, 34, 35, 36, 11, 12, 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, 38, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 7 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237596 none COC1=C2OC(C(=O)[O-])=CC2=C(C=C2CC3=CC=C(C#N)C=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 3, 3, 3, 1, 6, 6, 6, 6, 6, 6, 1, 1] 6 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 25, 26, 38, 30, 37] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237596 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237596 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237596/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237596 Building REAL300000237597 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237597' /scratch/stefan/7769818/working/building/REAL300000237597 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237597 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237597/0 /scratch/stefan/7769818/working/building/REAL300000237597 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/597 `/scratch/stefan/7769818/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=CC=C1OCCC(=O)[O-]) `REAL300000237597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237597 none COC1=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 35, 79, 94, 94, 94, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 79, 79, 94, 94] 94 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 36, 31] set([0, 1, 2, 3, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42]) total number of confs: 340 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237597 none COC1=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 37, 51, 66, 66, 4, 4, 4, 1, 5, 5, 5, 5, 5, 5, 1, 1, 37, 37, 51, 51] 94 rigid atoms, others: [1, 2, 3, 4, 5, 38, 18, 19, 20, 21, 30, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237597 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237597 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237597/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237597 Building REAL300000237598 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237598' /scratch/stefan/7769818/working/building/REAL300000237598 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237598 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237598/0 /scratch/stefan/7769818/working/building/REAL300000237598 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/598 `/scratch/stefan/7769818/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(C(=O)[O-])C=C3Cl)C(=O)C2=C1) `REAL300000237598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237598 none N#CC1=CC=C2CC(=CC3=CC=C(C(=O)[O-])C=C3Cl)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3] 3 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 7 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237598 none N#CC1=CC=C2CC(=CC3=CC=C(C(=O)[O-])C=C3Cl)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237598 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237598 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237598/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237598 Building REAL300000237599 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237599' /scratch/stefan/7769818/working/building/REAL300000237599 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237599 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237599/0 /scratch/stefan/7769818/working/building/REAL300000237599 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/599 `/scratch/stefan/7769818/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=CC(C(=O)[O-])=C3Cl)C(=O)C2=C1) `REAL300000237599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237599 none N#CC1=CC=C2CC(=CC3=CC=CC(C(=O)[O-])=C3Cl)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 6] 6 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237599 none N#CC1=CC=C2CC(=CC3=CC=CC(C(=O)[O-])=C3Cl)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 1] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30]) total number of confs: 7 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237599 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237599 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237599/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237599 Building REAL300000237600 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237600' /scratch/stefan/7769818/working/building/REAL300000237600 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237600 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237600/0 /scratch/stefan/7769818/working/building/REAL300000237600 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/600 `/scratch/stefan/7769818/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(O)C(C(=O)[O-])=C3)C(=O)C2=C1) `REAL300000237600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237600 none N#CC1=CC=C2CC(=CC3=CC=C(O)C(C(=O)[O-])=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 2, 1, 4] 8 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237600 none N#CC1=CC=C2CC(=CC3=CC=C(O)C(C(=O)[O-])=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 4, 1] 8 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237600 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237600 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237600/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237600 Building REAL300000237601 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237601' /scratch/stefan/7769818/working/building/REAL300000237601 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237601 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237601/0 /scratch/stefan/7769818/working/building/REAL300000237601 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/601 `/scratch/stefan/7769818/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=C1CC2=CC=C(C#N)C=C2C1=O) `REAL300000237601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. 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 REAL300000237601 0 /scratch/stefan/7769818/working/building/REAL300000237601 /scratch/stefan/7769818/working /scratch/stefan/7769818 `0' -> `0.failed' Finished preparing REAL300000237601 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Found failed protomers Marking REAL300000237601 as failed mkdir: created directory `/scratch/stefan/7769818/failed' `/scratch/stefan/7769818/working/building/REAL300000237601' -> `/scratch/stefan/7769818/failed/REAL300000237601' Building REAL300000237602 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237602' /scratch/stefan/7769818/working/building/REAL300000237602 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237602 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237602/0 /scratch/stefan/7769818/working/building/REAL300000237602 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/602 `/scratch/stefan/7769818/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=C2CC3=CC=C(C#N)C=C3C2=O)C=C1)C(=O)[O-]) `REAL300000237602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237602 none CC(OC1=CC=C(C=C2CC3=CC=C(C#N)C=C3C2=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 16, 2, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 31, 31, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7] 31 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 103 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237602 none CC(OC1=CC=C(C=C2CC3=CC=C(C#N)C=C3C2=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', '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, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 16, 20, 20, 16, 16, 16, 16, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1] 31 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 38, 29, 30, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 80 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237602 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237602 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237602/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237602 Building REAL300000237603 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237603' /scratch/stefan/7769818/working/building/REAL300000237603 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237603 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237603/0 /scratch/stefan/7769818/working/building/REAL300000237603 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/603 `/scratch/stefan/7769818/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=CC=C3OCCC(=O)[O-])C(=O)C2=C1) `REAL300000237603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237603 none N#CC1=CC=C2CC(=CC3=CC=CC=C3OCCC(=O)[O-])C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 40, 66, 80, 77, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 40, 40, 66, 66, 6] 113 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 333 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237603 none N#CC1=CC=C2CC(=CC3=CC=CC=C3OCCC(=O)[O-])C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 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, 1, 1, 1, 6, 6, 2, 6, 6, 6, 35, 92, 113, 113, 112, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 92, 92, 113, 113, 1] 113 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([32, 33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31]) total number of confs: 413 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237603 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237603 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237603/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237603 Building REAL300000237604 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237604' /scratch/stefan/7769818/working/building/REAL300000237604 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237604 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237604/0 /scratch/stefan/7769818/working/building/REAL300000237604 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/604 `/scratch/stefan/7769818/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=CC(OC(C(=O)[O-])C4=CC=CC=C4)=C3)C(=O)C2=C1) `REAL300000237604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237604 none N#CC1=CC=C2CC(=CC3=CC=CC(OC(C(=O)[O-])C4=CC=CC=C4)=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 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: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 13, 45, 63, 63, 45, 67, 67, 45, 67, 67, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 45, 67, 67, 45, 67, 67, 1, 7] 201 rigid atoms, others: [35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 45]) total number of confs: 333 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237604 none N#CC1=CC=C2CC(=CC3=CC=CC(OC(C(=O)[O-])C4=CC=CC=C4)=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 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: [201, 201, 201, 201, 201, 201, 201, 201, 67, 67, 67, 67, 67, 13, 4, 1, 4, 5, 5, 1, 1, 1, 1, 1, 1, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 67, 67, 67, 4, 1, 1, 1, 1, 1, 67, 201] 201 rigid atoms, others: [39, 40, 41, 42, 43, 15, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45]) total number of confs: 456 number of broken/clashed sets: 32 ./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: REAL300000237604 none N#CC1=CC=C2CC(=CC3=CC=CC(OC(C(=O)[O-])C4=CC=CC=C4)=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 57, 172, 201, 201, 172, 201, 201, 172, 201, 201, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 172, 201, 201, 172, 201, 201, 7, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 45, 26, 32, 33, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 808 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237604 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237604 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237604/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237604 Building REAL300000237605 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237605' /scratch/stefan/7769818/working/building/REAL300000237605 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237605 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237605/0 /scratch/stefan/7769818/working/building/REAL300000237605 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/605 `/scratch/stefan/7769818/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(C(=O)[O-])C(F)=C3)C(=O)C2=C1) `REAL300000237605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237605 none N#CC1=CC=C2CC(=CC3=CC=C(C(=O)[O-])C(F)=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 3, 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, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3] 3 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237605 none N#CC1=CC=C2CC(=CC3=CC=C(C(=O)[O-])C(F)=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237605 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237605 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237605/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237605 Building REAL300000237606 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237606' /scratch/stefan/7769818/working/building/REAL300000237606 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237606 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237606/0 /scratch/stefan/7769818/working/building/REAL300000237606 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/606 `/scratch/stefan/7769818/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(C=CC(=O)[O-])O3)C(=O)C2=C1) `REAL300000237606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237606 none N#CC1=CC=C2CC(=CC3=CC=C(C=CC(=O)[O-])O3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 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, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 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: [8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 8, 8, 8] 22 rigid atoms, others: [8, 9, 10, 11, 12, 13, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237606 none N#CC1=CC=C2CC(=CC3=CC=C(C=CC(=O)[O-])O3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 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, 7, 7, 7, 7, 7, 2, 2, 3, 7, 3, 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, 8, 8, 8, 8, 22, 22, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 22, 22, 1] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237606 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237606 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237606/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237606 Building REAL300000237607 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237607' /scratch/stefan/7769818/working/building/REAL300000237607 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237607 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237607/0 /scratch/stefan/7769818/working/building/REAL300000237607 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/607 `/scratch/stefan/7769818/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=C2CC3=CC=C(C#N)C=C3C2=O)C=C1C(=O)[O-]) `REAL300000237607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237607 none COC1=CC=C(C=C2CC3=CC=C(C#N)C=C3C2=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 12, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 7] 12 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 35, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237607 none COC1=CC=C(C=C2CC3=CC=C(C#N)C=C3C2=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 7, 7, 7, 7, 7, 7, 1] 12 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 27, 28, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237607 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237607 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237607/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237607 Building REAL300000237608 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237608' /scratch/stefan/7769818/working/building/REAL300000237608 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237608 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237608/0 /scratch/stefan/7769818/working/building/REAL300000237608 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/608 `/scratch/stefan/7769818/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC(C(=O)[O-])=CC=C3F)C(=O)C2=C1) `REAL300000237608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237608 none N#CC1=CC=C2CC(=CC3=CC(C(=O)[O-])=CC=C3F)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7] 7 rigid atoms, others: [8, 9, 10, 11, 12, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237608 none N#CC1=CC=C2CC(=CC3=CC(C(=O)[O-])=CC=C3F)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30]) total number of confs: 8 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237608 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237608 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237608/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237608 Building REAL300000237609 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237609' /scratch/stefan/7769818/working/building/REAL300000237609 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237609 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237609/0 /scratch/stefan/7769818/working/building/REAL300000237609 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/609 `/scratch/stefan/7769818/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C(=O)[O-])C=C1C=C1CC2=CC=C(C#N)C=C2C1=O) `REAL300000237609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237609 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=C1CC2=CC=C(C#N)C=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 7, 7, 7, 7, 12, 7, 7, 12, 12, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 7, 12, 12, 12, 7, 1, 1, 1, 1, 1, 1] 22 rigid atoms, others: [34, 35, 36, 37, 38, 39, 12, 13, 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, 33, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237609 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=C1CC2=CC=C(C#N)C=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 1, 1, 3, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 1, 3, 3, 3, 1, 7, 7, 7, 7, 7, 7] 22 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 11, 12, 13, 33, 29] set([0, 6, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237609 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237609 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237609/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237609 Building REAL300000237610 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237610' /scratch/stefan/7769818/working/building/REAL300000237610 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237610 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237610/0 /scratch/stefan/7769818/working/building/REAL300000237610 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/610 `/scratch/stefan/7769818/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(F)C(C(=O)[O-])=C3)C(=O)C2=C1) `REAL300000237610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237610 none N#CC1=CC=C2CC(=CC3=CC=C(F)C(C(=O)[O-])=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 11, 1, 1, 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, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7] 7 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237610 none N#CC1=CC=C2CC(=CC3=CC=C(F)C(C(=O)[O-])=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 11, 1, 1, 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, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30]) total number of confs: 8 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237610 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237610 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237610/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237610 Building REAL300000237611 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237611' /scratch/stefan/7769818/working/building/REAL300000237611 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237611 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237611/0 /scratch/stefan/7769818/working/building/REAL300000237611 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/611 `/scratch/stefan/7769818/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(CC(=O)[O-])C=C3)C(=O)C2=C1) `REAL300000237611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237611 none N#CC1=CC=C2CC(=CC3=CC=C(CC(=O)[O-])C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 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, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 1, 1, 2] 3 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, 34]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237611 none N#CC1=CC=C2CC(=CC3=CC=C(CC(=O)[O-])C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 2, 2, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34] set([32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237611 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237611 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237611/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237611 Building REAL300000237612 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237612' /scratch/stefan/7769818/working/building/REAL300000237612 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237612 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237612/0 /scratch/stefan/7769818/working/building/REAL300000237612 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/612 `/scratch/stefan/7769818/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC(Br)=CC(C(=O)[O-])=C3)C(=O)C2=C1) `REAL300000237612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237612 none N#CC1=CC=C2CC(=CC3=CC(Br)=CC(C(=O)[O-])=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 1, 11, 1, 1, 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, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7] 7 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237612 none N#CC1=CC=C2CC(=CC3=CC(Br)=CC(C(=O)[O-])=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 1, 11, 1, 1, 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, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30]) total number of confs: 8 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237612 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237612 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237612/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237612 Building REAL300000237613 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237613' /scratch/stefan/7769818/working/building/REAL300000237613 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237613 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237613/0 /scratch/stefan/7769818/working/building/REAL300000237613 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/613 `/scratch/stefan/7769818/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(C=CC(=O)[O-])C=C3)C(=O)C2=C1) `REAL300000237613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237613 none N#CC1=CC=C2CC(=CC3=CC=C(C=CC(=O)[O-])C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 5, 5, 1, 1, 4] 7 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35]) total number of confs: 23 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237613 none N#CC1=CC=C2CC(=CC3=CC=C(C=CC(=O)[O-])C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 4, 4, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35] set([32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 24 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237613 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237613 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237613/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237613 Building REAL300000237614 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237614' /scratch/stefan/7769818/working/building/REAL300000237614 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237614 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237614/0 /scratch/stefan/7769818/working/building/REAL300000237614 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/614 `/scratch/stefan/7769818/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC(F)=C(C(=O)[O-])C=C3F)C(=O)C2=C1) `REAL300000237614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237614 none N#CC1=CC=C2CC(=CC3=CC(F)=C(C(=O)[O-])C=C3F)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 7] 7 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237614 none N#CC1=CC=C2CC(=CC3=CC(F)=C(C(=O)[O-])C=C3F)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237614 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237614 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237614/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237614 Building REAL300000237615 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237615' /scratch/stefan/7769818/working/building/REAL300000237615 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237615 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237615/0 /scratch/stefan/7769818/working/building/REAL300000237615 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/615 `/scratch/stefan/7769818/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=C4C(=CC=C3)NN=C4C(=O)[O-])C(=O)C2=C1) `REAL300000237615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237615 none N#CC1=CC=C2CC(=CC3=C4C(=CC=C3)NN=C4C(=O)[O-])C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6] 6 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237615 none N#CC1=CC=C2CC(=CC3=C4C(=CC=C3)NN=C4C(=O)[O-])C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31]) total number of confs: 7 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237615 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237615 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237615/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237615 Building REAL300000237616 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237616' /scratch/stefan/7769818/working/building/REAL300000237616 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237616 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237616/0 /scratch/stefan/7769818/working/building/REAL300000237616 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/616 `/scratch/stefan/7769818/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CN(CC(=O)[O-])N=C3C3=CC=CC=C3)C(=O)C2=C1) `REAL300000237616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237616 none N#CC1=CC=C2CC(=CC3=CN(CC(=O)[O-])N=C3C3=CC=CC=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 12, 12, 1, 1, 1, 6, 6, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 6, 6, 1, 6, 6, 7] 32 rigid atoms, others: [33, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237616 none N#CC1=CC=C2CC(=CC3=CN(CC(=O)[O-])N=C3C3=CC=CC=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 19, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 19, 19, 1, 1, 1, 1, 1, 19] 32 rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41]) total number of confs: 111 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: REAL300000237616 none N#CC1=CC=C2CC(=CC3=CN(CC(=O)[O-])N=C3C3=CC=CC=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 28, 28, 7, 7, 7, 19, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 25, 25, 19, 19, 9, 19, 19, 1] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 41, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237616 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237616 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237616/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237616 Building REAL300000237617 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237617' /scratch/stefan/7769818/working/building/REAL300000237617 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237617 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237617/0 /scratch/stefan/7769818/working/building/REAL300000237617 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/617 `/scratch/stefan/7769818/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2=NN(CC(=O)[O-])C=C2C=C2CC3=CC=C(C#N)C=C3C2=O)C=C1) `REAL300000237617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237617 none COC1=CC=C(C2=NN(CC(=O)[O-])C=C2C=C2CC3=CC=C(C#N)C=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 8, 8, 1, 7, 7, 7, 7, 7, 7, 11, 11] 60 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237617 none COC1=CC=C(C2=NN(CC(=O)[O-])C=C2C=C2CC3=CC=C(C#N)C=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [30, 7, 7, 30, 30, 7, 7, 7, 7, 7, 30, 37, 37, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 7, 1, 1, 1, 1, 1, 1, 30, 30] 60 rigid atoms, others: [38, 39, 40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45]) total number of confs: 205 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: REAL300000237617 none COC1=CC=C(C2=NN(CC(=O)[O-])C=C2C=C2CC3=CC=C(C#N)C=C3C2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 11, 25, 32, 32, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 25, 25, 11, 30, 30, 30, 30, 30, 30, 1, 1] 60 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 28, 44, 34, 45, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 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 /scratch/stefan/7769818/working/building/REAL300000237617 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237617 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237617/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237617 Building REAL300000237618 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237618' /scratch/stefan/7769818/working/building/REAL300000237618 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237618 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237618/0 /scratch/stefan/7769818/working/building/REAL300000237618 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/618 `/scratch/stefan/7769818/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(C(=O)[O-])C(O)=C4)O3)C(=O)C2=C1) `REAL300000237618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237618 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(C(=O)[O-])C(O)=C4)O3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 10, 10, 7, 7, 7, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 7, 7, 14, 7, 8] 86 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237618 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(C(=O)[O-])C(O)=C4)O3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 43, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 7, 43, 43, 43, 43, 43, 43, 43, 43, 43, 7, 7, 1, 1, 2, 1, 43] 86 rigid atoms, others: [35, 36, 38, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 39]) total number of confs: 100 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: REAL300000237618 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(C(=O)[O-])C(O)=C4)O3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 43, 43, 43, 43, 43, 43, 43, 43, 43, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 43, 43, 86, 43, 1] 86 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([33, 34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237618 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237618 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237618/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237618 Building REAL300000237619 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237619' /scratch/stefan/7769818/working/building/REAL300000237619 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237619 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237619/0 /scratch/stefan/7769818/working/building/REAL300000237619 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/619 `/scratch/stefan/7769818/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)C=C3)C(=O)C2=C1) `REAL300000237619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237619 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', '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', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 3, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 3, 3, 3, 3, 1, 1, 2] 3 rigid atoms, others: [33, 34, 39, 8, 9, 10, 11, 12, 13, 40, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 41]) total number of confs: 18 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237619 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', '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', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3] 3 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 15 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: REAL300000237619 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', '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', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 2, 2, 3, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 2, 2, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 41, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 12 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237619 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237619 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237619/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237619 Building REAL300000237620 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237620' /scratch/stefan/7769818/working/building/REAL300000237620 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237620 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237620/0 /scratch/stefan/7769818/working/building/REAL300000237620 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/620 `/scratch/stefan/7769818/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CNC4=CC=C(C(=O)[O-])C=C34)C(=O)C2=C1) `REAL300000237620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237620 none N#CC1=CC=C2CC(=CC3=CNC4=CC=C(C(=O)[O-])C=C34)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6] 6 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 35, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237620 none N#CC1=CC=C2CC(=CC3=CNC4=CC=C(C(=O)[O-])C=C34)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31]) total number of confs: 7 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237620 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237620 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237620/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237620 Building REAL300000237621 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237621' /scratch/stefan/7769818/working/building/REAL300000237621 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237621 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237621/0 /scratch/stefan/7769818/working/building/REAL300000237621 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/621 `/scratch/stefan/7769818/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000237621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237621 none COC1=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [19, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 25, 47, 47, 52, 52, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 7, 47, 47, 47, 47] 52 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 36, 37] set([0, 1, 2, 3, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237621 none COC1=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [3, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 14, 14, 22, 22, 4, 4, 4, 1, 7, 7, 7, 7, 7, 7, 1, 14, 15, 15, 15] 52 rigid atoms, others: [1, 2, 3, 4, 5, 38, 18, 19, 20, 21, 22, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237621 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237621 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237621/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237621 Building REAL300000237622 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237622' /scratch/stefan/7769818/working/building/REAL300000237622 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237622 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237622/0 /scratch/stefan/7769818/working/building/REAL300000237622 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/622 `/scratch/stefan/7769818/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(C(=O)[O-])C(O)=C3)C(=O)C2=C1) `REAL300000237622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237622 none N#CC1=CC=C2CC(=CC3=CC=C(C(=O)[O-])C(O)=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 2, 1, 3] 6 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 18, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237622 none N#CC1=CC=C2CC(=CC3=CC=C(C(=O)[O-])C(O)=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 3, 1] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237622 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237622 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237622/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237622 Building REAL300000237623 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237623' /scratch/stefan/7769818/working/building/REAL300000237623 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237623 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237623/0 /scratch/stefan/7769818/working/building/REAL300000237623 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/623 `/scratch/stefan/7769818/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=C2CC3=CC=C(C#N)C=C3C2=O)C=C1C(=O)[O-]) `REAL300000237623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237623 none CC1=CC=C(C=C2CC3=CC=C(C#N)C=C3C2=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 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, 7, 7, 3, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7] 7 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 34, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237623 none CC1=CC=C(C=C2CC3=CC=C(C#N)C=C3C2=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 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, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 7, 7, 7, 7, 7, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 18, 19, 20, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237623 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237623 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237623/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237623 Building REAL300000237624 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237624' /scratch/stefan/7769818/working/building/REAL300000237624 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237624 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237624/0 /scratch/stefan/7769818/working/building/REAL300000237624 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/624 `/scratch/stefan/7769818/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC(C(=O)[O-])=C(Cl)S3)C(=O)C2=C1) `REAL300000237624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237624 none N#CC1=CC=C2CC(=CC3=CC(C(=O)[O-])=C(Cl)S3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7] 7 rigid atoms, others: [8, 9, 10, 11, 12, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237624 none N#CC1=CC=C2CC(=CC3=CC(C(=O)[O-])=C(Cl)S3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 27]) total number of confs: 8 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237624 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237624 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237624/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237624 Building REAL300000237625 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237625' /scratch/stefan/7769818/working/building/REAL300000237625 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237625 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237625/0 /scratch/stefan/7769818/working/building/REAL300000237625 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/625 `/scratch/stefan/7769818/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)S3)C(=O)C2=C1) `REAL300000237625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237625 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)S3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 3, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5] 8 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237625 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)S3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 8] 8 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 20 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: REAL300000237625 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)S3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 1] 8 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237625 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237625 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237625/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237625 Building REAL300000237626 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237626' /scratch/stefan/7769818/working/building/REAL300000237626 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237626 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237626/0 /scratch/stefan/7769818/working/building/REAL300000237626 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/626 `/scratch/stefan/7769818/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(O)C(C(=O)[O-])=C4)O3)C(=O)C2=C1) `REAL300000237626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237626 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(O)C(C(=O)[O-])=C4)O3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 9, 9, 18, 9, 8] 78 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237626 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(O)C(C(=O)[O-])=C4)O3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [39, 39, 39, 39, 39, 39, 39, 39, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 39, 39, 39, 39, 39, 39, 39, 39, 39, 9, 9, 1, 1, 2, 1, 39] 78 rigid atoms, others: [35, 36, 38, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 39]) total number of confs: 88 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: REAL300000237626 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=C(O)C(C(=O)[O-])=C4)O3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 1, 1, 1, 8, 8, 8, 8, 39, 39, 39, 39, 39, 39, 39, 39, 39, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 39, 39, 78, 39, 1] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([33, 34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237626 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237626 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237626/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237626 Building REAL300000237627 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237627' /scratch/stefan/7769818/working/building/REAL300000237627 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237627 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237627/0 /scratch/stefan/7769818/working/building/REAL300000237627 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/627 `/scratch/stefan/7769818/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=CC(C(=O)[O-])=C4)S3)C(=O)C2=C1) `REAL300000237627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237627 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=CC(C(=O)[O-])=C4)S3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 11, 11, 11, 11, 7] 20 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 26 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237627 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=CC(C(=O)[O-])=C4)S3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 1, 1, 1, 1, 20] 20 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 46 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: REAL300000237627 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=CC(C(=O)[O-])=C4)S3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 1] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237627 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237627 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237627/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237627 Building REAL300000237628 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237628' /scratch/stefan/7769818/working/building/REAL300000237628 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237628 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237628/0 /scratch/stefan/7769818/working/building/REAL300000237628 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/628 `/scratch/stefan/7769818/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=C1CC2=CC=C(C#N)C=C2C1=O) `REAL300000237628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237628 none COC1=CC=C(C(=O)[O-])C=C1C=C1CC2=CC=C(C#N)C=C2C1=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', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1] 7 rigid atoms, others: [32, 33, 34, 35, 10, 11, 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, 24, 25, 26, 27, 28, 29]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237628 none COC1=CC=C(C(=O)[O-])C=C1C=C1CC2=CC=C(C#N)C=C2C1=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', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7] 7 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 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: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237628 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237628 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237628/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237628 Building REAL300000237629 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237629' /scratch/stefan/7769818/working/building/REAL300000237629 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237629 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237629/0 /scratch/stefan/7769818/working/building/REAL300000237629 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/629 `/scratch/stefan/7769818/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CSC4=CC=C(C(=O)[O-])C=C34)C(=O)C2=C1) `REAL300000237629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237629 none N#CC1=CC=C2CC(=CC3=CSC4=CC=C(C(=O)[O-])C=C34)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 7, 7, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6] 6 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237629 none N#CC1=CC=C2CC(=CC3=CSC4=CC=C(C(=O)[O-])C=C34)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 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, 7, 7, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31]) total number of confs: 7 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237629 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237629 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237629/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237629 Building REAL300000237630 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237630' /scratch/stefan/7769818/working/building/REAL300000237630 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237630 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237630/0 /scratch/stefan/7769818/working/building/REAL300000237630 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/630 `/scratch/stefan/7769818/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC(C(=O)[O-])=CC=C3Br)C(=O)C2=C1) `REAL300000237630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237630 none N#CC1=CC=C2CC(=CC3=CC(C(=O)[O-])=CC=C3Br)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 6] 6 rigid atoms, others: [8, 9, 10, 11, 12, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237630 none N#CC1=CC=C2CC(=CC3=CC(C(=O)[O-])=CC=C3Br)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 1] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30]) total number of confs: 7 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237630 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237630 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237630/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237630 Building REAL300000237631 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237631' /scratch/stefan/7769818/working/building/REAL300000237631 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237631 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237631/0 /scratch/stefan/7769818/working/building/REAL300000237631 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/631 `/scratch/stefan/7769818/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(C(=O)[O-])C=C3[N+](=O)[O-])C(=O)C2=C1) `REAL300000237631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237631 none N#CC1=CC=C2CC(=CC3=CC=C(C(=O)[O-])C=C3[N+](=O)[O-])C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 3, 3, 7, 3, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3] 3 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237631 none N#CC1=CC=C2CC(=CC3=CC=C(C(=O)[O-])C=C3[N+](=O)[O-])C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237631 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237631 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237631/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237631 Building REAL300000237632 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237632' /scratch/stefan/7769818/working/building/REAL300000237632 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237632 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237632/0 /scratch/stefan/7769818/working/building/REAL300000237632 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/632 `/scratch/stefan/7769818/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=CC(CC(=O)[O-])=C3)C(=O)C2=C1) `REAL300000237632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237632 none N#CC1=CC=C2CC(=CC3=CC=CC(CC(=O)[O-])=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', '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, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 2, 2, 1, 7] 12 rigid atoms, others: [33, 8, 9, 10, 11, 12, 13, 14, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 34]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237632 none N#CC1=CC=C2CC(=CC3=CC=CC(CC(=O)[O-])=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'O.2', '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, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 1, 7, 7, 12, 12, 12, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 12, 12, 7, 1] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34] set([32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237632 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237632 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237632/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237632 Building REAL300000237633 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237633' /scratch/stefan/7769818/working/building/REAL300000237633 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237633 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237633/0 /scratch/stefan/7769818/working/building/REAL300000237633 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/633 `/scratch/stefan/7769818/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=CC=C1C(=O)[O-]) `REAL300000237633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237633 none COC1=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 1, 1, 1, 1, 1, 1, 7, 7] 9 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 35, 34, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 20 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237633 none COC1=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 7, 7, 7, 7, 7, 7, 1, 1] 9 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 18, 19, 20, 21, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237633 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237633 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237633/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237633 Building REAL300000237634 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237634' /scratch/stefan/7769818/working/building/REAL300000237634 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237634 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237634/0 /scratch/stefan/7769818/working/building/REAL300000237634 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/634 `/scratch/stefan/7769818/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=C(F)C=C(C(=O)[O-])C=C3F)C(=O)C2=C1) `REAL300000237634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237634 none N#CC1=CC=C2CC(=CC3=C(F)C=C(C(=O)[O-])C=C3F)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2] 2 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 9 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237634 none N#CC1=CC=C2CC(=CC3=C(F)C=C(C(=O)[O-])C=C3F)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1] 2 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237634 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237634 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237634/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237634 Building REAL300000237635 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237635' /scratch/stefan/7769818/working/building/REAL300000237635 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237635 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237635/0 /scratch/stefan/7769818/working/building/REAL300000237635 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/635 `/scratch/stefan/7769818/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=C(F)C=CC(C(=O)[O-])=C3F)C(=O)C2=C1) `REAL300000237635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237635 none N#CC1=CC=C2CC(=CC3=C(F)C=CC(C(=O)[O-])=C3F)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 1, 15, 1, 11, 1, 1, 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, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 7] 7 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237635 none N#CC1=CC=C2CC(=CC3=C(F)C=CC(C(=O)[O-])=C3F)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 1, 15, 1, 11, 1, 1, 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, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30]) total number of confs: 8 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237635 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237635 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237635/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237635 Building REAL300000237636 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237636' /scratch/stefan/7769818/working/building/REAL300000237636 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237636 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237636/0 /scratch/stefan/7769818/working/building/REAL300000237636 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/636 `/scratch/stefan/7769818/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=CC(CC(=O)[O-])=C4)C=C3)C(=O)C2=C1) `REAL300000237636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237636 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=CC(CC(=O)[O-])=C4)C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 3, 5, 5, 9, 12, 12, 5, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 5, 5, 3, 9, 9, 5, 1, 1, 4] 20 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 54 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237636 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=CC(CC(=O)[O-])=C4)C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 2, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5, 12] 20 rigid atoms, others: [36, 37, 38, 41, 12, 13, 14, 15, 16, 17, 18, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 42, 43, 44]) total number of confs: 56 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: REAL300000237636 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=CC(CC(=O)[O-])=C4)C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 4, 4, 1, 1, 11, 11, 3, 11, 11, 19, 20, 20, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 6, 19, 19, 11, 4, 4, 1] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237636 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237636 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237636/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237636 Building REAL300000237637 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237637' /scratch/stefan/7769818/working/building/REAL300000237637 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237637 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237637/0 /scratch/stefan/7769818/working/building/REAL300000237637 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/637 `/scratch/stefan/7769818/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=CC=C1OCC(=O)[O-]) `REAL300000237637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237637 none CCOC1=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 39, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 47, 133, 159, 159, 95, 95, 95, 95, 95, 7, 1, 1, 1, 1, 1, 1, 7, 7, 133, 133] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 38, 37] set([0, 1, 2, 3, 4, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42]) total number of confs: 789 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237637 none CCOC1=CC(C=C2CC3=CC=C(C#N)C=C3C2=O)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 9, 40, 70, 70, 34, 34, 34, 33, 33, 1, 7, 7, 7, 7, 7, 7, 1, 1, 40, 40] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 40, 19, 20, 21, 22] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 348 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237637 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237637 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237637/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237637 Building REAL300000237638 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237638' /scratch/stefan/7769818/working/building/REAL300000237638 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237638 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237638/0 /scratch/stefan/7769818/working/building/REAL300000237638 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/638 `/scratch/stefan/7769818/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC(F)=C(C(=O)[O-])C(F)=C3)C(=O)C2=C1) `REAL300000237638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237638 none N#CC1=CC=C2CC(=CC3=CC(F)=C(C(=O)[O-])C(F)=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 4] 4 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237638 none N#CC1=CC=C2CC(=CC3=CC(F)=C(C(=O)[O-])C(F)=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1] 4 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30]) total number of confs: 5 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237638 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237638 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237638/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237638 Building REAL300000237639 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237639' /scratch/stefan/7769818/working/building/REAL300000237639 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237639 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237639/0 /scratch/stefan/7769818/working/building/REAL300000237639 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/639 `/scratch/stefan/7769818/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC4=C(C=C(C(=O)[O-])N4)O3)C(=O)C2=C1) `REAL300000237639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237639 none N#CC1=CC=C2CC(=CC3=CC4=C(C=C(C(=O)[O-])N4)O3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 5] 5 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237639 none N#CC1=CC=C2CC(=CC3=CC4=C(C=C(C(=O)[O-])N4)O3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 6 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237639 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237639 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237639/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237639 Building REAL300000237640 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237640' /scratch/stefan/7769818/working/building/REAL300000237640 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237640 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237640/0 /scratch/stefan/7769818/working/building/REAL300000237640 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/640 `/scratch/stefan/7769818/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C4OC(C(=O)[O-])=CC4=C3)C(=O)C2=C1) `REAL300000237640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237640 none N#CC1=CC=C2CC(=CC3=CC=C4OC(C(=O)[O-])=CC4=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 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, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3] 3 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237640 none N#CC1=CC=C2CC(=CC3=CC=C4OC(C(=O)[O-])=CC4=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 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, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31]) total number of confs: 4 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237640 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237640 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237640/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237640 Building REAL300000237641 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237641' /scratch/stefan/7769818/working/building/REAL300000237641 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237641 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237641/0 /scratch/stefan/7769818/working/building/REAL300000237641 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/641 `/scratch/stefan/7769818/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=CN4C(C(=O)[O-])=CN=C34)C(=O)C2=C1) `REAL300000237641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237641 none N#CC1=CC=C2CC(=CC3=CC=CN4C(C(=O)[O-])=CN=C34)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6] 6 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237641 none N#CC1=CC=C2CC(=CC3=CC=CN4C(C(=O)[O-])=CN=C34)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31]) total number of confs: 7 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237641 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237641 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237641/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237641 Building REAL300000237642 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237642' /scratch/stefan/7769818/working/building/REAL300000237642 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237642 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237642/0 /scratch/stefan/7769818/working/building/REAL300000237642 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/642 `/scratch/stefan/7769818/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=C1CC2=CC=C(C#N)C=C2C1=O) `REAL300000237642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237642 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=C1CC2=CC=C(C#N)C=C2C1=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', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1] 7 rigid atoms, others: [34, 35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 8 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237642 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=C1CC2=CC=C(C#N)C=C2C1=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', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 7 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([4, 5, 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: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237642 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237642 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237642/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237642 Building REAL300000237643 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237643' /scratch/stefan/7769818/working/building/REAL300000237643 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237643 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237643/0 /scratch/stefan/7769818/working/building/REAL300000237643 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/643 `/scratch/stefan/7769818/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CN=C4C=CC(C(=O)[O-])=CN34)C(=O)C2=C1) `REAL300000237643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237643 none N#CC1=CC=C2CC(=CC3=CN=C4C=CC(C(=O)[O-])=CN34)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 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, 7, 7, 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 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7] 7 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237643 none N#CC1=CC=C2CC(=CC3=CN=C4C=CC(C(=O)[O-])=CN34)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 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, 7, 7, 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 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31]) total number of confs: 8 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237643 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237643 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237643/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237643 Building REAL300000237644 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237644' /scratch/stefan/7769818/working/building/REAL300000237644 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237644 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237644/0 /scratch/stefan/7769818/working/building/REAL300000237644 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/644 `/scratch/stefan/7769818/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(N4C=NC(C(=O)[O-])=C4)C=C3)C(=O)C2=C1) `REAL300000237644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237644 none N#CC1=CC=C2CC(=CC3=CC=C(N4C=NC(C(=O)[O-])=C4)C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 7, 7, 1, 1, 4] 7 rigid atoms, others: [32, 33, 36, 37, 8, 9, 10, 11, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38]) total number of confs: 16 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237644 none N#CC1=CC=C2CC(=CC3=CC=C(N4C=NC(C(=O)[O-])=C4)C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 7, 7, 7] 7 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 30 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: REAL300000237644 none N#CC1=CC=C2CC(=CC3=CC=C(N4C=NC(C(=O)[O-])=C4)C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', '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, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 4, 4, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237644 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237644 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237644/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237644 Building REAL300000237645 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237645' /scratch/stefan/7769818/working/building/REAL300000237645 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237645 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237645/0 /scratch/stefan/7769818/working/building/REAL300000237645 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/645 `/scratch/stefan/7769818/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=CC(C(=O)[O-])=C3F)C(=O)C2=C1) `REAL300000237645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237645 none N#CC1=CC=C2CC(=CC3=CC=CC(C(=O)[O-])=C3F)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 6] 6 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237645 none N#CC1=CC=C2CC(=CC3=CC=CC(C(=O)[O-])=C3F)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 1] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30]) total number of confs: 7 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237645 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237645 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237645/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237645 Building REAL300000237646 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237646' /scratch/stefan/7769818/working/building/REAL300000237646 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237646 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237646/0 /scratch/stefan/7769818/working/building/REAL300000237646 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/646 `/scratch/stefan/7769818/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(OCC(=O)[O-])C(Cl)=C3)C(=O)C2=C1) `REAL300000237646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237646 none N#CC1=CC=C2CC(=CC3=CC=C(OCC(=O)[O-])C(Cl)=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.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.2', 'O.2', '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, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 11, 1, 1, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 7, 28, 37, 37, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 28, 28, 1, 7] 52 rigid atoms, others: [34, 8, 9, 10, 11, 12, 13, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35]) total number of confs: 139 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237646 none N#CC1=CC=C2CC(=CC3=CC=C(OCC(=O)[O-])C(Cl)=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.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.2', 'O.2', '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, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 11, 1, 1, 7, 7, 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, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 2, 6, 30, 52, 52, 52, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 52, 52, 7, 1] 52 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237646 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237646 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237646/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237646 Building REAL300000237647 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237647' /scratch/stefan/7769818/working/building/REAL300000237647 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237647 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237647/0 /scratch/stefan/7769818/working/building/REAL300000237647 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/647 `/scratch/stefan/7769818/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(S(=O)(=O)NCC(=O)[O-])C=C3)C(=O)C2=C1) `REAL300000237647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237647 none N#CC1=CC=C2CC(=CC3=CC=C(S(=O)(=O)NCC(=O)[O-])C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 31, 34, 34, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 9, 31, 31, 1, 1, 4] 45 rigid atoms, others: [32, 33, 37, 38, 8, 9, 10, 11, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237647 none N#CC1=CC=C2CC(=CC3=CC=C(S(=O)(=O)NCC(=O)[O-])C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 7, 7, 7, 21, 45, 45, 45, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 21, 45, 45, 4, 4, 1] 45 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237647 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237647 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237647/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237647 Building REAL300000237648 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237648' /scratch/stefan/7769818/working/building/REAL300000237648 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237648 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237648/0 /scratch/stefan/7769818/working/building/REAL300000237648 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/648 `/scratch/stefan/7769818/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=CC=C4C(=O)[O-])C=C3)C(=O)C2=C1) `REAL300000237648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237648 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=CC=C4C(=O)[O-])C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 6, 6, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 5, 5, 5, 5, 1, 1, 4] 7 rigid atoms, others: [33, 34, 39, 8, 9, 10, 11, 12, 13, 40, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 41]) total number of confs: 18 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237648 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=CC=C4C(=O)[O-])C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 1, 1, 1, 1, 5, 5, 7] 7 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 32 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: REAL300000237648 none N#CC1=CC=C2CC(=CC3=CC=C(C4=CC=CC=C4C(=O)[O-])C=C3)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 2, 7, 7, 6, 7, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 4, 4, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 41, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237648 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237648 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237648/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237648 Building REAL300000237649 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237649' /scratch/stefan/7769818/working/building/REAL300000237649 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237649 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237649/0 /scratch/stefan/7769818/working/building/REAL300000237649 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/649 `/scratch/stefan/7769818/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=C1CC2=CC=C(C#N)C=C2C1=O) `REAL300000237649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237649 none COC1=CC(C(=O)[O-])=CC=C1C=C1CC2=CC=C(C#N)C=C2C1=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', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1] 5 rigid atoms, others: [32, 33, 34, 35, 10, 11, 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, 24, 25, 26, 27, 28, 29]) total number of confs: 6 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237649 none COC1=CC(C(=O)[O-])=CC=C1C=C1CC2=CC=C(C#N)C=C2C1=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', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5] 5 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 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: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237649 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237649 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237649/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237649 Building REAL300000237650 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237650' /scratch/stefan/7769818/working/building/REAL300000237650 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237650 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237650/0 /scratch/stefan/7769818/working/building/REAL300000237650 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/650 `/scratch/stefan/7769818/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C2CC(=CC3=C4C=C(C(=O)[O-])SC4=CC=C3F)C(=O)C2=C1) `REAL300000237650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237650 none N#CC1=CC=C2CC(=CC3=C4C=C(C(=O)[O-])SC4=CC=C3F)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7] 7 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237650 none N#CC1=CC=C2CC(=CC3=C4C=C(C(=O)[O-])SC4=CC=C3F)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31]) total number of confs: 8 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237650 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237650 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237650/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237650 Building REAL300000237651 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237651' /scratch/stefan/7769818/working/building/REAL300000237651 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237651 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237651/0 /scratch/stefan/7769818/working/building/REAL300000237651 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/651 `/scratch/stefan/7769818/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CC3=C(S2)N(C)N=C3C)=CC=C1OCC(=O)[O-]) `REAL300000237651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237651 none COC1=CC(C=CC(=O)C2=CC3=C(S2)N(C)N=C3C)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 8, 5, 8, 1, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 35, 35, 35, 13, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 34, 34, 110, 199, 201, 201, 66, 66, 66, 35, 12, 12, 1, 2, 2, 2, 2, 2, 2, 35, 35, 199, 199] 201 rigid atoms, others: [33, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 664 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237651 none COC1=CC(C=CC(=O)C2=CC3=C(S2)N(C)N=C3C)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 8, 5, 8, 1, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 9, 31, 51, 51, 3, 3, 3, 1, 5, 5, 35, 35, 35, 35, 35, 35, 35, 1, 1, 31, 31] 201 rigid atoms, others: [1, 2, 3, 4, 5, 40, 41, 19, 20, 21, 22, 30] set([0, 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, 42, 43]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237651 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237651 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237651/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237651 Building REAL300000237652 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237652' /scratch/stefan/7769818/working/building/REAL300000237652 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237652 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237652/0 /scratch/stefan/7769818/working/building/REAL300000237652 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/652 `/scratch/stefan/7769818/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])C=C1)S2) `REAL300000237652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237652 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])C=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 42, 42, 42, 19, 3, 19, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 3, 3, 1, 1, 1, 1] 42 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 75 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237652 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])C=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 2, 2, 2, 2, 2, 2, 1, 42, 42, 42, 42, 42, 42] 42 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237652 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237652 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237652/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237652 Building REAL300000237653 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237653' /scratch/stefan/7769818/working/building/REAL300000237653 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237653 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237653/0 /scratch/stefan/7769818/working/building/REAL300000237653 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/653 `/scratch/stefan/7769818/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(OCC(=O)[O-])C=C1)S2) `REAL300000237653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237653 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(OCC(=O)[O-])C=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 55, 15, 3, 15, 3, 1, 1, 1, 1, 1, 1, 6, 23, 32, 32, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 3, 3, 1, 1, 23, 23, 1, 1] 201 rigid atoms, others: [34, 35, 38, 39, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 183 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237653 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(OCC(=O)[O-])C=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 37, 37, 55, 55, 37, 55, 135, 201, 201, 201, 55, 55, 1, 2, 2, 2, 2, 2, 2, 1, 37, 37, 55, 55, 201, 201, 55, 55] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 689 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237653 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237653 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237653/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237653 Building REAL300000237654 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237654' /scratch/stefan/7769818/working/building/REAL300000237654 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237654 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237654/0 /scratch/stefan/7769818/working/building/REAL300000237654 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/654 `/scratch/stefan/7769818/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(OCCC(=O)[O-])C=C1)S2) `REAL300000237654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237654 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(OCCC(=O)[O-])C=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 54, 15, 3, 15, 3, 1, 1, 1, 1, 1, 1, 6, 21, 29, 44, 37, 1, 1, 54, 54, 54, 54, 54, 54, 54, 54, 3, 3, 1, 1, 21, 21, 29, 29, 1, 1] 201 rigid atoms, others: [35, 36, 41, 42, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 237 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237654 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(OCCC(=O)[O-])C=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 34, 34, 54, 54, 34, 54, 155, 189, 201, 201, 194, 54, 54, 1, 2, 2, 2, 2, 2, 2, 1, 34, 34, 54, 54, 189, 189, 201, 201, 54, 54] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 624 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237654 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237654 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237654/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237654 Building REAL300000237655 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237655' /scratch/stefan/7769818/working/building/REAL300000237655 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237655 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237655/0 /scratch/stefan/7769818/working/building/REAL300000237655 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/655 `/scratch/stefan/7769818/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(OC(C)C(=O)[O-])=C1)S2) `REAL300000237655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237655 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(OC(C)C(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 58, 58, 58, 58, 14, 5, 14, 5, 1, 1, 1, 1, 1, 1, 1, 11, 27, 27, 38, 38, 1, 58, 58, 58, 58, 58, 58, 58, 58, 5, 5, 1, 1, 1, 27, 27, 27, 27, 1] 201 rigid atoms, others: [35, 36, 37, 42, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 214 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237655 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(OC(C)C(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 27, 27, 58, 58, 58, 58, 58, 174, 201, 201, 201, 201, 58, 1, 2, 2, 2, 2, 2, 2, 1, 27, 27, 58, 58, 58, 201, 201, 201, 201, 58] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 446 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237655 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237655 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237655/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237655 Building REAL300000237656 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237656' /scratch/stefan/7769818/working/building/REAL300000237656 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237656 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237656/0 /scratch/stefan/7769818/working/building/REAL300000237656 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/656 `/scratch/stefan/7769818/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(OCCC(=O)[O-])=C1)S2) `REAL300000237656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237656 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(OCCC(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 54, 18, 6, 18, 6, 1, 1, 1, 1, 1, 1, 1, 7, 21, 23, 38, 32, 1, 54, 54, 54, 54, 54, 54, 54, 54, 6, 6, 1, 1, 1, 21, 21, 23, 23, 1] 201 rigid atoms, others: [35, 36, 37, 42, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 220 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237656 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(OCCC(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 21, 21, 54, 54, 54, 54, 54, 152, 199, 201, 201, 196, 54, 1, 2, 2, 2, 2, 2, 2, 1, 21, 21, 54, 54, 54, 199, 199, 201, 201, 54] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 500 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237656 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237656 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237656/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237656 Building REAL300000237657 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237657' /scratch/stefan/7769818/working/building/REAL300000237657 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237657 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237657/0 /scratch/stefan/7769818/working/building/REAL300000237657 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/657 `/scratch/stefan/7769818/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C3=CC=C(C(=O)[O-])C=C3)O1)S2) `REAL300000237657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237657 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C3=CC=C(C(=O)[O-])C=C3)O1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 14, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 150, 150, 150, 150, 150, 59, 13, 58, 13, 1, 1, 1, 1, 1, 1, 7, 7, 2, 2, 7, 7, 7, 7, 1, 150, 150, 150, 150, 150, 150, 150, 150, 13, 13, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237657 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C3=CC=C(C(=O)[O-])C=C3)O1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 14, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 144, 50, 144, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 201, 201, 201, 201, 201, 201, 201, 201, 50, 50, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 455 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: REAL300000237657 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C3=CC=C(C(=O)[O-])C=C3)O1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 14, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 64, 64, 150, 150, 150, 150, 201, 201, 157, 157, 201, 201, 201, 201, 150, 1, 2, 2, 2, 2, 2, 2, 1, 64, 64, 149, 150, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 683 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237657 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237657 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237657/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237657 Building REAL300000237658 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237658' /scratch/stefan/7769818/working/building/REAL300000237658 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237658 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237658/0 /scratch/stefan/7769818/working/building/REAL300000237658 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/658 `/scratch/stefan/7769818/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(OCC(=O)[O-])=C1)S2) `REAL300000237658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237658 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(OCC(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 59, 59, 59, 59, 15, 5, 15, 5, 1, 1, 1, 1, 1, 1, 1, 7, 23, 35, 35, 1, 59, 59, 59, 59, 59, 59, 59, 59, 5, 5, 1, 1, 1, 23, 23, 1] 201 rigid atoms, others: [34, 35, 36, 39, 12, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 206 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237658 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(OCC(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 31, 31, 59, 59, 59, 59, 59, 141, 201, 201, 201, 59, 1, 2, 2, 2, 2, 2, 2, 1, 31, 31, 59, 59, 59, 201, 201, 59] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 589 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237658 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237658 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237658/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237658 Building REAL300000237659 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237659' /scratch/stefan/7769818/working/building/REAL300000237659 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237659 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237659/0 /scratch/stefan/7769818/working/building/REAL300000237659 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/659 `/scratch/stefan/7769818/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(OC(F)(F)C(=O)[O-])C=C1)S2) `REAL300000237659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237659 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(OC(F)(F)C(=O)[O-])C=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 30, 11, 3, 11, 3, 1, 1, 1, 1, 1, 1, 12, 44, 44, 44, 71, 71, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 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, 33, 34, 35]) total number of confs: 282 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237659 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(OC(F)(F)C(=O)[O-])C=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 9, 9, 19, 19, 30, 30, 19, 30, 131, 201, 201, 201, 201, 201, 30, 30, 1, 2, 2, 2, 2, 2, 2, 1, 19, 19, 30, 30, 30, 30] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 26] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 594 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237659 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237659 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237659/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237659 Building REAL300000237660 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237660' /scratch/stefan/7769818/working/building/REAL300000237660 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237660 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237660/0 /scratch/stefan/7769818/working/building/REAL300000237660 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/660 `/scratch/stefan/7769818/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CC3=C(S2)N(C)N=C3C)C=C1) `REAL300000237660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237660 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CC3=C(S2)N(C)N=C3C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 8, 5, 8, 1, 5, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 68, 67, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 67, 68, 1, 2, 2, 2, 2, 2, 2, 201, 201] 201 rigid atoms, others: [34, 14, 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, 15, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 351 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237660 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CC3=C(S2)N(C)N=C3C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 8, 5, 8, 1, 5, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 9, 9, 60, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 3, 3, 3, 1, 9, 9, 201, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 41, 26, 27, 42, 31] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 330 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237660 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237660 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237660/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237660 Building REAL300000237661 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237661' /scratch/stefan/7769818/working/building/REAL300000237661 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237661 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237661/0 /scratch/stefan/7769818/working/building/REAL300000237661 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/661 `/scratch/stefan/7769818/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CN(CC(=O)[O-])N=N1)S2) `REAL300000237661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237661 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CN(CC(=O)[O-])N=N1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'S.3', '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, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 43, 44, 43, 44, 44, 16, 7, 15, 7, 1, 1, 1, 1, 1, 8, 12, 12, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 7, 7, 1, 8, 8] 58 rigid atoms, others: [32, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237661 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CN(CC(=O)[O-])N=N1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'S.3', '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, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 22, 22, 44, 44, 44, 58, 58, 58, 44, 44, 1, 2, 2, 2, 2, 2, 2, 1, 22, 22, 44, 58, 58] 58 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237661 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237661 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237661/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237661 Building REAL300000237662 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237662' /scratch/stefan/7769818/working/building/REAL300000237662 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237662 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237662/0 /scratch/stefan/7769818/working/building/REAL300000237662 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/662 `/scratch/stefan/7769818/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(C(=O)[O-])=C1)S2) `REAL300000237662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237662 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(C(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 96, 96, 96, 96, 40, 6, 40, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 96, 96, 96, 96, 96, 96, 96, 96, 6, 6, 1, 1, 1, 1] 96 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 181 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237662 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(C(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 58, 58, 96, 96, 96, 96, 96, 96, 96, 96, 1, 2, 2, 2, 2, 2, 2, 1, 58, 58, 96, 96, 96, 96] 96 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 218 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237662 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237662 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237662/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237662 Building REAL300000237663 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237663' /scratch/stefan/7769818/working/building/REAL300000237663 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237663 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237663/0 /scratch/stefan/7769818/working/building/REAL300000237663 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/663 `/scratch/stefan/7769818/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=CS1)S2) `REAL300000237663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237663 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=CS1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 14, 7, 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, 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 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 118, 118, 118, 118, 68, 12, 67, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 118, 118, 118, 118, 13, 12, 1, 1] 118 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237663 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=CS1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 14, 7, 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, 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 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 48, 48, 118, 118, 118, 118, 118, 118, 118, 1, 2, 2, 2, 2, 2, 2, 1, 48, 48, 118, 118] 118 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 28] set([32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237663 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237663 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237663/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237663 Building REAL300000237664 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237664' /scratch/stefan/7769818/working/building/REAL300000237664 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237664 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237664/0 /scratch/stefan/7769818/working/building/REAL300000237664 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/664 `/scratch/stefan/7769818/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])C=C1Cl)S2) `REAL300000237664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237664 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])C=C1Cl)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [101, 101, 101, 101, 101, 101, 101, 101, 60, 9, 60, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 101, 101, 101, 101, 101, 101, 101, 101, 9, 9, 1, 1, 1] 101 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 209 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237664 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])C=C1Cl)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 68, 68, 101, 101, 68, 101, 101, 101, 101, 101, 101, 1, 2, 2, 2, 2, 2, 2, 1, 68, 68, 101, 101, 101] 101 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 384 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237664 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237664 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237664/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237664 Building REAL300000237665 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237665' /scratch/stefan/7769818/working/building/REAL300000237665 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237665 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237665/0 /scratch/stefan/7769818/working/building/REAL300000237665 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/665 `/scratch/stefan/7769818/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(C(=O)[O-])=C1Cl)S2) `REAL300000237665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237665 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(C(=O)[O-])=C1Cl)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 162, 162, 162, 162, 162, 62, 9, 62, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 162, 162, 162, 162, 162, 162, 162, 162, 9, 9, 1, 1, 1] 162 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 283 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237665 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(C(=O)[O-])=C1Cl)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 1, 1, 1, 1, 1, 13, 13, 78, 78, 162, 162, 162, 162, 162, 162, 162, 162, 162, 1, 2, 2, 2, 2, 2, 2, 1, 78, 78, 154, 162, 162] 162 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 333 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237665 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237665 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237665/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237665 Building REAL300000237666 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237666' /scratch/stefan/7769818/working/building/REAL300000237666 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237666 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237666/0 /scratch/stefan/7769818/working/building/REAL300000237666 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/666 `/scratch/stefan/7769818/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(O)C(C(=O)[O-])=C1)S2) `REAL300000237666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237666 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(O)C(C(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 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: [101, 101, 101, 101, 101, 101, 101, 101, 41, 5, 41, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 101, 101, 101, 101, 101, 101, 101, 101, 5, 5, 1, 1, 2, 1] 202 rigid atoms, others: [33, 34, 36, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 189 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237666 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(O)C(C(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 61, 61, 101, 101, 101, 101, 101, 101, 101, 101, 101, 1, 2, 2, 2, 2, 2, 2, 1, 61, 61, 101, 101, 202, 101] 202 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 30] set([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: 430 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237666 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237666 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237666/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237666 Building REAL300000237667 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237667' /scratch/stefan/7769818/working/building/REAL300000237667 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237667 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237667/0 /scratch/stefan/7769818/working/building/REAL300000237667 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/667 `/scratch/stefan/7769818/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=C(C)C=C1C)S2) `REAL300000237667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237667 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=C(C)C=C1C)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 65, 9, 65, 9, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 2, 2, 2, 1, 2, 2, 2] 201 rigid atoms, others: [34, 38, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 39, 40, 41]) total number of confs: 354 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237667 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=C(C)C=C1C)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 77, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 1, 77, 77, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 368 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237667 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237667 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237667/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237667 Building REAL300000237668 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237668' /scratch/stefan/7769818/working/building/REAL300000237668 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237668 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237668/0 /scratch/stefan/7769818/working/building/REAL300000237668 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/668 `/scratch/stefan/7769818/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(OC(C)C(=O)[O-])C=C1)S2) `REAL300000237668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237668 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(OC(C)C(=O)[O-])C=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 61, 61, 61, 61, 19, 4, 18, 4, 1, 1, 1, 1, 1, 1, 11, 28, 28, 40, 40, 1, 1, 61, 61, 61, 61, 61, 61, 61, 61, 4, 4, 1, 1, 28, 28, 28, 28, 1, 1] 201 rigid atoms, others: [35, 36, 41, 42, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 230 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237668 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(OC(C)C(=O)[O-])C=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 36, 36, 61, 61, 36, 56, 174, 201, 201, 201, 201, 61, 61, 1, 2, 2, 2, 2, 2, 2, 1, 36, 36, 61, 61, 201, 201, 201, 201, 61, 61] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 578 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237668 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237668 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237668/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237668 Building REAL300000237669 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237669' /scratch/stefan/7769818/working/building/REAL300000237669 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237669 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237669/0 /scratch/stefan/7769818/working/building/REAL300000237669 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/669 `/scratch/stefan/7769818/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC=C1OCCC(=O)[O-])S2) `REAL300000237669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237669 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC=C1OCCC(=O)[O-])S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 75, 75, 75, 75, 75, 23, 7, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 25, 29, 50, 44, 75, 75, 75, 75, 75, 75, 75, 75, 7, 7, 1, 1, 1, 1, 25, 25, 29, 29] 201 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 304 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237669 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC=C1OCCC(=O)[O-])S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 34, 34, 75, 75, 43, 75, 75, 75, 156, 199, 201, 201, 197, 1, 2, 2, 2, 2, 2, 2, 1, 34, 34, 75, 75, 75, 75, 199, 199, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 647 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237669 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237669 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237669/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237669 Building REAL300000237670 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237670' /scratch/stefan/7769818/working/building/REAL300000237670 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237670 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237670/0 /scratch/stefan/7769818/working/building/REAL300000237670 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/670 `/scratch/stefan/7769818/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=C(C(=O)[O-])C=NN1C)S2) `REAL300000237670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237670 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=C(C(=O)[O-])C=NN1C)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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 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, 125, 125, 125, 43, 9, 43, 9, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 125, 125, 125, 125, 125, 125, 125, 125, 9, 9, 1, 2, 2, 2] 125 rigid atoms, others: [32, 12, 13, 14, 15, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 226 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237670 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=C(C(=O)[O-])C=NN1C)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 67, 67, 125, 125, 125, 125, 125, 125, 125, 125, 1, 2, 2, 2, 2, 2, 2, 1, 67, 67, 125, 125, 125, 125] 125 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 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 /scratch/stefan/7769818/working/building/REAL300000237670 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237670 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237670/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237670 Building REAL300000237671 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237671' /scratch/stefan/7769818/working/building/REAL300000237671 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237671 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237671/0 /scratch/stefan/7769818/working/building/REAL300000237671 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/671 `/scratch/stefan/7769818/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])C(F)=C1)S2) `REAL300000237671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237671 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])C(F)=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 141, 141, 141, 141, 141, 141, 41, 6, 41, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 141, 141, 141, 141, 141, 141, 141, 141, 6, 6, 1, 1, 1] 141 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 228 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237671 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])C(F)=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 70, 70, 141, 141, 141, 141, 141, 141, 141, 141, 141, 1, 2, 2, 2, 2, 2, 2, 1, 70, 70, 141, 141, 141] 141 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 288 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237671 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237671 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237671/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237671 Building REAL300000237672 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237672' /scratch/stefan/7769818/working/building/REAL300000237672 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237672 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237672/0 /scratch/stefan/7769818/working/building/REAL300000237672 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/672 `/scratch/stefan/7769818/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C=CC(=O)[O-])O1)S2) `REAL300000237672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237672 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C=CC(=O)[O-])O1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 136, 136, 136, 136, 136, 44, 12, 44, 12, 1, 1, 1, 1, 1, 1, 12, 12, 37, 37, 1, 136, 136, 136, 136, 136, 136, 136, 136, 12, 12, 1, 1, 12, 12] 201 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 327 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237672 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C=CC(=O)[O-])O1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 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, 13, 13, 59, 59, 136, 136, 136, 136, 201, 201, 201, 201, 136, 1, 2, 2, 2, 2, 2, 2, 1, 59, 59, 136, 136, 199, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 30] set([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: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237672 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237672 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237672/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237672 Building REAL300000237673 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237673' /scratch/stefan/7769818/working/building/REAL300000237673 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237673 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237673/0 /scratch/stefan/7769818/working/building/REAL300000237673 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/673 `/scratch/stefan/7769818/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC(=O)C2=CC3=C(S2)N(C)N=C3C)C=C1C(=O)[O-]) `REAL300000237673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237673 none COC1=CC=C(C=CC(=O)C2=CC3=C(S2)N(C)N=C3C)C=C1C(=O)[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.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 8, 5, 8, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 123, 123, 123, 123, 56, 55, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 201, 201, 201, 201, 201, 123, 123, 55, 56, 1, 2, 2, 2, 2, 2, 2, 123] 201 rigid atoms, others: [32, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 719 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237673 none COC1=CC=C(C=CC(=O)C2=CC3=C(S2)N(C)N=C3C)C=C1C(=O)[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.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 8, 5, 8, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 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, 31, 31, 123, 123, 123, 123, 123, 123, 123, 123, 123, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 5, 5, 123, 123, 123, 123, 123, 123, 123, 1] 201 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: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237673 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237673 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237673/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237673 Building REAL300000237674 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237674' /scratch/stefan/7769818/working/building/REAL300000237674 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237674 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237674/0 /scratch/stefan/7769818/working/building/REAL300000237674 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/674 `/scratch/stefan/7769818/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=CC=C1F)S2) `REAL300000237674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237674 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=CC=C1F)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 144, 144, 144, 144, 144, 144, 77, 11, 77, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 144, 144, 144, 144, 144, 144, 144, 144, 11, 11, 1, 1, 1] 144 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 283 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237674 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=CC=C1F)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 71, 71, 144, 144, 144, 144, 144, 144, 144, 144, 144, 1, 2, 2, 2, 2, 2, 2, 1, 71, 71, 144, 144, 144] 144 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 292 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237674 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237674 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237674/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237674 Building REAL300000237675 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237675' /scratch/stefan/7769818/working/building/REAL300000237675 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237675 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237675/0 /scratch/stefan/7769818/working/building/REAL300000237675 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/675 `/scratch/stefan/7769818/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC2=C(S1)N(C)N=C2C) `REAL300000237675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237675 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC2=C(S1)N(C)N=C2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 105, 105, 105, 105, 105, 159, 105, 105, 149, 149, 105, 33, 32, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 146, 146, 146, 105, 159, 159, 159, 105, 32, 33, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [37, 15, 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, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 547 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237675 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC2=C(S1)N(C)N=C2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 3, 3, 1, 1, 1, 9, 9, 31, 31, 105, 105, 105, 105, 105, 105, 105, 105, 105, 3, 3, 3, 1, 3, 3, 3, 1, 9, 9, 105, 105, 105, 105, 105, 105, 105] 201 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 11, 12, 34, 13, 30] set([0, 6, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237675 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237675 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237675/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237675 Building REAL300000237676 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237676' /scratch/stefan/7769818/working/building/REAL300000237676 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237676 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237676/0 /scratch/stefan/7769818/working/building/REAL300000237676 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/676 `/scratch/stefan/7769818/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(F)C(C(=O)[O-])=C1)S2) `REAL300000237676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237676 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(F)C(C(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 168, 168, 168, 168, 41, 5, 41, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 168, 168, 168, 168, 168, 168, 168, 168, 5, 5, 1, 1, 1] 168 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 258 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237676 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(F)C(C(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 1, 1, 12, 12, 76, 76, 168, 168, 168, 168, 168, 168, 168, 168, 168, 1, 2, 2, 2, 2, 2, 2, 1, 76, 76, 168, 168, 168] 168 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 333 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237676 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237676 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237676/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237676 Building REAL300000237677 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237677' /scratch/stefan/7769818/working/building/REAL300000237677 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237677 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237677/0 /scratch/stefan/7769818/working/building/REAL300000237677 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/677 `/scratch/stefan/7769818/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(CC(=O)[O-])C=C1)S2) `REAL300000237677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237677 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(CC(=O)[O-])C=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.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, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [91, 91, 91, 91, 91, 91, 91, 91, 21, 3, 21, 3, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 91, 91, 91, 91, 91, 91, 91, 91, 3, 3, 1, 1, 2, 2, 1, 1] 116 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: 157 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237677 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(CC(=O)[O-])C=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.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, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 13, 74, 74, 91, 91, 74, 75, 116, 116, 116, 91, 91, 1, 2, 2, 2, 2, 2, 2, 1, 74, 74, 91, 91, 116, 116, 91, 91] 116 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 30] set([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, 37, 38]) total number of confs: 491 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237677 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237677 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237677/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237677 Building REAL300000237678 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237678' /scratch/stefan/7769818/working/building/REAL300000237678 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237678 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237678/0 /scratch/stefan/7769818/working/building/REAL300000237678 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/678 `/scratch/stefan/7769818/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])S1)S2) `REAL300000237678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237678 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])S1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 14, 7, 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, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 100, 100, 100, 100, 61, 12, 60, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 100, 100, 100, 13, 12, 1, 1] 100 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 216 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237678 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])S1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 14, 7, 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, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 53, 53, 100, 100, 100, 100, 100, 100, 100, 1, 2, 2, 2, 2, 2, 2, 1, 53, 53, 100, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 28] set([32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237678 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237678 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237678/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237678 Building REAL300000237679 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237679' /scratch/stefan/7769818/working/building/REAL300000237679 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237679 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237679/0 /scratch/stefan/7769818/working/building/REAL300000237679 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/679 `/scratch/stefan/7769818/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C=CC(=O)[O-])C=C1)S2) `REAL300000237679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237679 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C=CC(=O)[O-])C=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', '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, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 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: [113, 113, 113, 113, 113, 113, 113, 113, 24, 3, 24, 3, 1, 1, 1, 1, 1, 1, 5, 5, 23, 23, 1, 1, 113, 113, 113, 113, 113, 113, 113, 113, 3, 3, 1, 1, 5, 5, 1, 1] 157 rigid atoms, others: [34, 35, 38, 39, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 218 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237679 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C=CC(=O)[O-])C=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', '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, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 85, 85, 113, 113, 85, 85, 155, 156, 157, 157, 113, 113, 1, 2, 2, 2, 2, 2, 2, 1, 85, 85, 113, 113, 155, 155, 113, 113] 157 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 589 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237679 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237679 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237679/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237679 Building REAL300000237680 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237680' /scratch/stefan/7769818/working/building/REAL300000237680 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237680 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237680/0 /scratch/stefan/7769818/working/building/REAL300000237680 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/680 `/scratch/stefan/7769818/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(F)=C(C(=O)[O-])C=C1F)S2) `REAL300000237680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237680 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(F)=C(C(=O)[O-])C=C1F)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'S.3', '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, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 14, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 79, 11, 79, 11, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 1, 1] 201 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 359 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237680 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(F)=C(C(=O)[O-])C=C1F)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'S.3', '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, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 14, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 74, 74, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 1, 74, 74, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 366 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237680 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237680 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237680/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237680 Building REAL300000237681 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237681' /scratch/stefan/7769818/working/building/REAL300000237681 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237681 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237681/0 /scratch/stefan/7769818/working/building/REAL300000237681 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/681 `/scratch/stefan/7769818/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=C3C(=CC=C1)NN=C3C(=O)[O-])S2) `REAL300000237681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237681 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=C3C(=CC=C1)NN=C3C(=O)[O-])S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 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, 132, 59, 9, 59, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 132, 132, 132, 132, 132, 132, 132, 132, 9, 9, 1, 1, 1, 1] 132 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237681 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=C3C(=CC=C1)NN=C3C(=O)[O-])S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.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, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 67, 67, 132, 132, 132, 132, 132, 132, 132, 132, 132, 132, 132, 1, 2, 2, 2, 2, 2, 2, 1, 67, 67, 132, 132, 132, 132] 132 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237681 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237681 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237681/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237681 Building REAL300000237682 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237682' /scratch/stefan/7769818/working/building/REAL300000237682 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237682 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237682/0 /scratch/stefan/7769818/working/building/REAL300000237682 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/682 `/scratch/stefan/7769818/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CNC3=CC=C(C(=O)[O-])C=C13)S2) `REAL300000237682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237682 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CNC3=CC=C(C(=O)[O-])C=C13)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 155, 155, 155, 155, 155, 75, 11, 75, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 155, 155, 155, 155, 155, 155, 155, 155, 11, 11, 1, 1, 1, 1, 1] 155 rigid atoms, others: [35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 308 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237682 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CNC3=CC=C(C(=O)[O-])C=C13)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 62, 62, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 1, 2, 2, 2, 2, 2, 2, 1, 62, 62, 155, 155, 155, 155, 155] 155 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237682 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237682 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237682/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237682 Building REAL300000237683 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237683' /scratch/stefan/7769818/working/building/REAL300000237683 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237683 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237683/0 /scratch/stefan/7769818/working/building/REAL300000237683 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/683 `/scratch/stefan/7769818/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])N=C1)S2) `REAL300000237683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237683 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])N=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 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, 80, 37, 5, 37, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 80, 80, 80, 5, 5, 1, 1, 1] 80 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 148 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237683 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])N=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 62, 62, 80, 80, 80, 80, 80, 80, 80, 80, 1, 2, 2, 2, 2, 2, 2, 1, 62, 62, 80, 80, 80] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 197 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237683 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237683 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237683/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237683 Building REAL300000237684 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237684' /scratch/stefan/7769818/working/building/REAL300000237684 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237684 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237684/0 /scratch/stefan/7769818/working/building/REAL300000237684 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/684 `/scratch/stefan/7769818/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])C(O)=C1)S2) `REAL300000237684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237684 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])C(O)=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 115, 115, 115, 115, 115, 115, 115, 46, 6, 46, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 115, 115, 115, 115, 115, 115, 115, 115, 6, 6, 1, 1, 2, 1] 230 rigid atoms, others: [33, 34, 36, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 203 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237684 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])C(O)=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 70, 70, 115, 115, 115, 115, 115, 115, 115, 115, 115, 1, 2, 2, 2, 2, 2, 2, 1, 70, 70, 115, 115, 230, 115] 230 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 30] set([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: 485 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237684 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237684 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237684/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237684 Building REAL300000237685 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237685' /scratch/stefan/7769818/working/building/REAL300000237685 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237685 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237685/0 /scratch/stefan/7769818/working/building/REAL300000237685 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/685 `/scratch/stefan/7769818/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C)C(C(=O)[O-])=C1)S2) `REAL300000237685.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237685 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C)C(C(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 109, 109, 109, 109, 109, 45, 5, 45, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 109, 109, 109, 109, 109, 109, 109, 109, 5, 5, 1, 1, 2, 2, 2, 1] 109 rigid atoms, others: [33, 34, 38, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 207 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237685 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C)C(C(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 63, 63, 109, 109, 109, 109, 109, 109, 109, 109, 109, 1, 2, 2, 2, 2, 2, 2, 1, 63, 63, 109, 109, 109, 109, 109, 109] 109 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 30] set([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, 37, 38]) total number of confs: 244 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237685 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237685 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237685/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237685 Building REAL300000237686 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237686' /scratch/stefan/7769818/working/building/REAL300000237686 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237686 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237686/0 /scratch/stefan/7769818/working/building/REAL300000237686 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/686 `/scratch/stefan/7769818/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=C(Cl)S1)S2) `REAL300000237686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237686 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=C(Cl)S1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 14, 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, 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, 201, 201, 201, 201, 201, 201, 86, 12, 86, 12, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 12, 12, 1] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 368 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237686 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=C(Cl)S1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 14, 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, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 55, 55, 201, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 1, 55, 55, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 29] set([32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237686 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237686 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237686/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237686 Building REAL300000237687 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237687' /scratch/stefan/7769818/working/building/REAL300000237687 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237687 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237687/0 /scratch/stefan/7769818/working/building/REAL300000237687 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/687 `/scratch/stefan/7769818/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=C(C)O1)S2) `REAL300000237687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237687 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=C(C)O1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 121, 121, 121, 121, 121, 53, 13, 52, 13, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 121, 121, 121, 121, 121, 121, 121, 121, 13, 13, 1, 2, 2, 2] 121 rigid atoms, others: [32, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 234 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237687 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=C(C)O1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 65, 65, 121, 121, 121, 121, 121, 121, 121, 121, 1, 2, 2, 2, 2, 2, 2, 1, 65, 65, 121, 121, 121, 121] 121 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 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 /scratch/stefan/7769818/working/building/REAL300000237687 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237687 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237687/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237687 Building REAL300000237688 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237688' /scratch/stefan/7769818/working/building/REAL300000237688 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237688 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237688/0 /scratch/stefan/7769818/working/building/REAL300000237688 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/688 `/scratch/stefan/7769818/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=NN1C)S2) `REAL300000237688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237688 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=NN1C)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 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, 102, 102, 102, 102, 102, 54, 10, 54, 10, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 102, 102, 102, 102, 102, 102, 102, 102, 10, 10, 1, 2, 2, 2] 102 rigid atoms, others: [32, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 211 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237688 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=NN1C)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 55, 55, 102, 102, 102, 102, 102, 102, 102, 102, 1, 2, 2, 2, 2, 2, 2, 1, 55, 55, 102, 102, 102, 102] 102 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237688 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237688 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237688/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237688 Building REAL300000237689 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237689' /scratch/stefan/7769818/working/building/REAL300000237689 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237689 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237689/0 /scratch/stefan/7769818/working/building/REAL300000237689 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/689 `/scratch/stefan/7769818/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CN=CC(C(=O)[O-])=C1)S2) `REAL300000237689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237689 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CN=CC(C(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', '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, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 95, 95, 95, 39, 5, 39, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 95, 95, 95, 95, 95, 95, 95, 95, 5, 5, 1, 1, 1] 95 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 177 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237689 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CN=CC(C(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', '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, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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, 13, 13, 53, 53, 95, 95, 95, 95, 95, 95, 95, 95, 1, 2, 2, 2, 2, 2, 2, 1, 53, 53, 95, 95, 95] 95 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 212 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237689 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237689 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237689/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237689 Building REAL300000237690 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237690' /scratch/stefan/7769818/working/building/REAL300000237690 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237690 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237690/0 /scratch/stefan/7769818/working/building/REAL300000237690 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/690 `/scratch/stefan/7769818/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=CO1)S2) `REAL300000237690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237690 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=CO1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 14, 7, 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, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 85, 85, 85, 85, 85, 55, 12, 55, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 85, 85, 85, 12, 12, 1, 1] 85 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 178 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237690 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(C(=O)[O-])=CO1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 14, 7, 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, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 54, 54, 85, 85, 85, 85, 85, 85, 85, 1, 2, 2, 2, 2, 2, 2, 1, 54, 54, 85, 85] 85 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 28] set([32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237690 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237690 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237690/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237690 Building REAL300000237691 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237691' /scratch/stefan/7769818/working/building/REAL300000237691 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237691 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237691/0 /scratch/stefan/7769818/working/building/REAL300000237691 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/691 `/scratch/stefan/7769818/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC2=C(S1)N(C)N=C2C) `REAL300000237691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237691 none COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC2=C(S1)N(C)N=C2C 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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 64, 63, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 63, 64, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 349 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237691 none COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC2=C(S1)N(C)N=C2C 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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 9, 9, 67, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 3, 3, 3, 1, 1, 1, 9, 9, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 28, 29, 30] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 342 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237691 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237691 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237691/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237691 Building REAL300000237692 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237692' /scratch/stefan/7769818/working/building/REAL300000237692 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237692 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237692/0 /scratch/stefan/7769818/working/building/REAL300000237692 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/692 `/scratch/stefan/7769818/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CSC3=CC=C(C(=O)[O-])C=C13)S2) `REAL300000237692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237692 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CSC3=CC=C(C(=O)[O-])C=C13)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 146, 146, 146, 146, 68, 9, 68, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 146, 146, 146, 146, 9, 9, 1, 1, 1, 1] 146 rigid atoms, others: [35, 36, 37, 38, 12, 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, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237692 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CSC3=CC=C(C(=O)[O-])C=C13)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 56, 56, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 1, 2, 2, 2, 2, 2, 2, 1, 56, 56, 146, 146, 146, 146] 146 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237692 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237692 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237692/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237692 Building REAL300000237693 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237693' /scratch/stefan/7769818/working/building/REAL300000237693 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237693 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237693/0 /scratch/stefan/7769818/working/building/REAL300000237693 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/693 `/scratch/stefan/7769818/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])C=C1[N+](=O)[O-])S2) `REAL300000237693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237693 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])C=C1[N+](=O)[O-])S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 96, 96, 96, 96, 39, 5, 39, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 96, 96, 96, 96, 96, 96, 96, 96, 5, 5, 1, 1, 1] 96 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237693 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(C(=O)[O-])C=C1[N+](=O)[O-])S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 73, 73, 96, 96, 73, 96, 96, 96, 96, 96, 96, 96, 96, 1, 2, 2, 2, 2, 2, 2, 1, 73, 73, 96, 96, 96] 96 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237693 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237693 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237693/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237693 Building REAL300000237694 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237694' /scratch/stefan/7769818/working/building/REAL300000237694 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237694 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237694/0 /scratch/stefan/7769818/working/building/REAL300000237694 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/694 `/scratch/stefan/7769818/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(CC(=O)[O-])=C1)S2) `REAL300000237694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237694 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(CC(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 137, 137, 137, 137, 137, 137, 137, 42, 5, 42, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 137, 137, 137, 137, 137, 137, 137, 137, 5, 5, 1, 1, 1, 2, 2, 1] 201 rigid atoms, others: [33, 34, 35, 38, 12, 13, 14, 15, 16, 17, 18, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 242 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237694 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(CC(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 13, 13, 64, 64, 137, 137, 103, 137, 137, 201, 201, 201, 137, 1, 2, 2, 2, 2, 2, 2, 1, 64, 64, 137, 137, 109, 201, 201, 137] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 30] set([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, 37, 38]) total number of confs: 783 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237694 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237694 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237694/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237694 Building REAL300000237695 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237695' /scratch/stefan/7769818/working/building/REAL300000237695 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237695 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237695/0 /scratch/stefan/7769818/working/building/REAL300000237695 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/695 `/scratch/stefan/7769818/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CC3=C(S2)N(C)N=C3C)=CC=C1C(=O)[O-]) `REAL300000237695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237695 none COC1=CC(C=CC(=O)C2=CC3=C(S2)N(C)N=C3C)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 8, 5, 8, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 162, 162, 162, 63, 62, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 201, 201, 201, 201, 201, 162, 62, 62, 1, 2, 2, 2, 2, 2, 2, 162, 162] 201 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 550 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237695 none COC1=CC(C=CC(=O)C2=CC3=C(S2)N(C)N=C3C)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 8, 5, 8, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 3, 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 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, 6, 6, 42, 42, 162, 162, 162, 162, 162, 162, 162, 162, 162, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 6, 6, 162, 162, 162, 162, 162, 162, 162, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 19, 20, 21, 22, 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, 35, 36, 37]) total number of confs: 258 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237695 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237695 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237695/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237695 Building REAL300000237696 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237696' /scratch/stefan/7769818/working/building/REAL300000237696 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237696 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237696/0 /scratch/stefan/7769818/working/building/REAL300000237696 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/696 `/scratch/stefan/7769818/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=C(F)C=C(C(=O)[O-])C=C1F)S2) `REAL300000237696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237696 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=C(F)C=C(C(=O)[O-])C=C1F)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'S.3', '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, 11, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 14, 7, 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, 7, 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 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, 67, 67, 67, 36, 6, 36, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 67, 67, 6, 6, 1, 1] 67 rigid atoms, others: [34, 35, 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, 33]) total number of confs: 133 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237696 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=C(F)C=C(C(=O)[O-])C=C1F)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'S.3', '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, 11, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 14, 7, 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, 7, 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 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 49, 49, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 1, 2, 2, 2, 2, 2, 2, 1, 49, 49, 66, 66] 66 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237696 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237696 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237696/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237696 Building REAL300000237697 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237697' /scratch/stefan/7769818/working/building/REAL300000237697 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237697 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237697/0 /scratch/stefan/7769818/working/building/REAL300000237697 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/697 `/scratch/stefan/7769818/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=C(F)C=CC(C(=O)[O-])=C1F)S2) `REAL300000237697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237697 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=C(F)C=CC(C(=O)[O-])=C1F)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'S.3', '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, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 1, 15, 14, 7, 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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 71, 11, 71, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 1, 1] 201 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 339 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237697 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=C(F)C=CC(C(=O)[O-])=C1F)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'S.3', '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, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 1, 15, 14, 7, 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, 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 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, 13, 13, 69, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 1, 69, 69, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237697 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237697 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237697/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237697 Building REAL300000237698 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237698' /scratch/stefan/7769818/working/building/REAL300000237698 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237698 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237698/0 /scratch/stefan/7769818/working/building/REAL300000237698 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/698 `/scratch/stefan/7769818/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CSC(C(=O)[O-])=C1)S2) `REAL300000237698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237698 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CSC(C(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 90, 90, 90, 36, 6, 36, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 90, 90, 90, 90, 90, 90, 90, 90, 6, 6, 1, 1] 90 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237698 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CSC(C(=O)[O-])=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 13, 13, 63, 63, 90, 90, 90, 90, 90, 90, 90, 1, 2, 2, 2, 2, 2, 2, 1, 63, 63, 90, 90] 90 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 28] set([32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237698 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237698 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237698/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237698 Building REAL300000237699 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237699' /scratch/stefan/7769818/working/building/REAL300000237699 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237699 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237699/0 /scratch/stefan/7769818/working/building/REAL300000237699 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/699 `/scratch/stefan/7769818/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(F)=C(C(=O)[O-])C(F)=C1)S2) `REAL300000237699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237699 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(F)=C(C(=O)[O-])C(F)=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.3', '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, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 91, 91, 91, 91, 23, 3, 23, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 91, 91, 91, 91, 91, 91, 91, 91, 3, 3, 1, 1] 91 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 145 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237699 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC(F)=C(C(=O)[O-])C(F)=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.3', '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, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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 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, 13, 13, 65, 65, 91, 91, 91, 65, 91, 91, 91, 91, 91, 91, 1, 2, 2, 2, 2, 2, 2, 1, 65, 65, 91, 91] 91 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 349 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237699 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237699 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237699/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237699 Building REAL300000237700 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237700' /scratch/stefan/7769818/working/building/REAL300000237700 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237700 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237700/0 /scratch/stefan/7769818/working/building/REAL300000237700 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/700 `/scratch/stefan/7769818/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC3=C(C=C(C(=O)[O-])N3)O1)S2) `REAL300000237700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237700 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC3=C(C=C(C(=O)[O-])N3)O1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.3', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 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: [58, 58, 58, 58, 58, 58, 58, 58, 31, 10, 30, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 58, 58, 58, 58, 58, 58, 58, 57, 10, 10, 1, 1, 1] 58 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 126 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237700 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC3=C(C=C(C(=O)[O-])N3)O1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.3', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 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, 1, 1, 1, 1, 1, 1, 13, 13, 43, 43, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 2, 2, 2, 2, 2, 2, 1, 43, 43, 58, 58, 58] 58 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237700 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237700 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237700/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237700 Building REAL300000237701 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237701' /scratch/stefan/7769818/working/building/REAL300000237701 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237701 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237701/0 /scratch/stefan/7769818/working/building/REAL300000237701 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/701 `/scratch/stefan/7769818/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C3OC(C(=O)[O-])=CC3=C1)S2) `REAL300000237701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237701 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C3OC(C(=O)[O-])=CC3=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 88, 88, 88, 88, 39, 6, 39, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 88, 88, 88, 88, 88, 88, 88, 88, 6, 6, 1, 1, 1, 1] 88 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 164 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237701 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C3OC(C(=O)[O-])=CC3=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 57, 57, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 1, 2, 2, 2, 2, 2, 2, 1, 57, 57, 88, 88, 88, 88] 88 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 206 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237701 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237701 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237701/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237701 Building REAL300000237702 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237702' /scratch/stefan/7769818/working/building/REAL300000237702 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237702 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237702/0 /scratch/stefan/7769818/working/building/REAL300000237702 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/702 `/scratch/stefan/7769818/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CN3C(C(=O)[O-])=CN=C13)S2) `REAL300000237702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237702 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CN3C(C(=O)[O-])=CN=C13)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 131, 131, 131, 131, 131, 69, 11, 69, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 131, 131, 131, 131, 131, 131, 131, 131, 11, 11, 1, 1, 1, 1] 131 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 266 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237702 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CN3C(C(=O)[O-])=CN=C13)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 63, 63, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 1, 2, 2, 2, 2, 2, 2, 1, 63, 63, 131, 131, 131, 131] 131 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237702 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237702 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237702/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237702 Building REAL300000237703 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237703' /scratch/stefan/7769818/working/building/REAL300000237703 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237703 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237703/0 /scratch/stefan/7769818/working/building/REAL300000237703 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/703 `/scratch/stefan/7769818/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=NC3=CC=CC=C3C(C(=O)[O-])=C1C)S2) `REAL300000237703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237703 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=NC3=CC=CC=C3C(C(=O)[O-])=C1C)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 110, 110, 110, 110, 110, 54, 9, 54, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 110, 110, 110, 110, 110, 110, 110, 110, 9, 9, 1, 1, 1, 1, 2, 2, 2] 110 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43]) total number of confs: 223 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237703 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=NC3=CC=CC=C3C(C(=O)[O-])=C1C)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 13, 62, 62, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 1, 2, 2, 2, 2, 2, 2, 1, 62, 62, 110, 110, 110, 110, 110, 110, 110] 110 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237703 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237703 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237703/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237703 Building REAL300000237704 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237704' /scratch/stefan/7769818/working/building/REAL300000237704 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237704 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237704/0 /scratch/stefan/7769818/working/building/REAL300000237704 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/704 `/scratch/stefan/7769818/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CN=C3C=CC(C(=O)[O-])=CN13)S2) `REAL300000237704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237704 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CN=C3C=CC(C(=O)[O-])=CN13)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 165, 165, 165, 165, 165, 83, 11, 83, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 165, 165, 165, 165, 165, 165, 165, 165, 11, 11, 1, 1, 1, 1] 165 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 319 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237704 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CN=C3C=CC(C(=O)[O-])=CN13)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 69, 69, 165, 165, 165, 165, 165, 165, 165, 165, 165, 165, 165, 1, 2, 2, 2, 2, 2, 2, 1, 69, 69, 165, 165, 165, 165] 165 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237704 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237704 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237704/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237704 Building REAL300000237705 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237705' /scratch/stefan/7769818/working/building/REAL300000237705 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237705 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237705/0 /scratch/stefan/7769818/working/building/REAL300000237705 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/705 `/scratch/stefan/7769818/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(N3C=NC(C(=O)[O-])=C3)C=C1)S2) `REAL300000237705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237705 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(N3C=NC(C(=O)[O-])=C3)C=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', '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, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 90, 90, 90, 24, 4, 24, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 90, 90, 90, 90, 90, 90, 90, 90, 4, 4, 1, 1, 11, 11, 1, 1] 139 rigid atoms, others: [37, 38, 41, 42, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 150 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237705 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(N3C=NC(C(=O)[O-])=C3)C=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', '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, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 139, 139, 139, 139, 139, 80, 20, 80, 20, 2, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 139, 139, 139, 139, 139, 139, 139, 139, 20, 20, 11, 11, 1, 1, 11, 11] 139 rigid atoms, others: [39, 40, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 310 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: REAL300000237705 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(N3C=NC(C(=O)[O-])=C3)C=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', '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, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 67, 67, 90, 90, 67, 67, 139, 139, 139, 139, 139, 139, 139, 90, 90, 1, 2, 2, 2, 2, 2, 2, 1, 67, 67, 90, 90, 139, 139, 90, 90] 139 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 403 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237705 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237705 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237705/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237705 Building REAL300000237706 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237706' /scratch/stefan/7769818/working/building/REAL300000237706 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237706 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237706/0 /scratch/stefan/7769818/working/building/REAL300000237706 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/706 `/scratch/stefan/7769818/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(C(=O)[O-])=C1F)S2) `REAL300000237706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237706 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(C(=O)[O-])=C1F)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 201, 201, 201, 201, 63, 11, 63, 11, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 336 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237706 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=CC(C(=O)[O-])=C1F)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'S.3', '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, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 66, 66, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 1, 66, 66, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 30] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 344 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237706 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237706 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237706/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237706 Building REAL300000237707 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237707' /scratch/stefan/7769818/working/building/REAL300000237707 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237707 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237707/0 /scratch/stefan/7769818/working/building/REAL300000237707 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/707 `/scratch/stefan/7769818/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(OCC(=O)[O-])C(Cl)=C1)S2) `REAL300000237707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237707 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(OCC(=O)[O-])C(Cl)=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 58, 58, 58, 58, 16, 5, 16, 5, 1, 1, 1, 1, 1, 1, 7, 29, 39, 39, 1, 1, 1, 58, 58, 58, 58, 58, 58, 58, 58, 5, 5, 1, 1, 29, 29, 1] 201 rigid atoms, others: [35, 36, 39, 12, 13, 14, 15, 16, 17, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 219 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237707 none CC1=NN(C)C2=C1C=C(C(=O)C=CC1=CC=C(OCC(=O)[O-])C(Cl)=C1)S2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 21, 21, 58, 58, 58, 58, 151, 201, 201, 201, 58, 58, 58, 1, 2, 2, 2, 2, 2, 2, 1, 21, 21, 58, 58, 201, 201, 58] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 507 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237707 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237707 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237707/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237707 Building REAL300000237708 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237708' /scratch/stefan/7769818/working/building/REAL300000237708 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237708 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237708/0 /scratch/stefan/7769818/working/building/REAL300000237708 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/708 `/scratch/stefan/7769818/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC2=C(S1)N(C)N=C2C) `REAL300000237708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237708 none COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC2=C(S1)N(C)N=C2C 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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 197, 197, 197, 197, 197, 197, 197, 86, 85, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 197, 197, 85, 85, 1, 2, 2, 2, 2, 2, 2] 197 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 375 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237708 none COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC2=C(S1)N(C)N=C2C 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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 79, 79, 197, 197, 197, 197, 197, 197, 197, 197, 197, 4, 4, 4, 1, 1, 1, 11, 11, 197, 197, 197, 197, 197, 197, 197] 197 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: 359 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237708 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237708 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237708/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237708 Building REAL300000237709 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237709' /scratch/stefan/7769818/working/building/REAL300000237709 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237709 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237709/0 /scratch/stefan/7769818/working/building/REAL300000237709 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/709 `/scratch/stefan/7769818/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CC=C(Br)N=C2)=CC=C1OCC(=O)[O-]) `REAL300000237709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237709 none COC1=CC(C=CC(=O)C2=CC=C(Br)N=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 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, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 43, 43, 43, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 133, 200, 201, 201, 75, 75, 75, 43, 17, 17, 1, 1, 1, 43, 43, 200, 200] 201 rigid atoms, others: [32, 7, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 612 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237709 none COC1=CC(C=CC(=O)C2=CC=C(Br)N=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 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, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 9, 29, 44, 44, 3, 3, 3, 1, 5, 5, 43, 43, 43, 1, 1, 29, 29] 201 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 16, 17, 18, 19, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237709 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237709 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237709/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237709 Building REAL300000237710 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237710' /scratch/stefan/7769818/working/building/REAL300000237710 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237710 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237710/0 /scratch/stefan/7769818/working/building/REAL300000237710 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/710 `/scratch/stefan/7769818/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1) `REAL300000237710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237710 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 1, 1, 1, 33, 33] 33 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 85 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237710 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 3, 3, 33, 33, 33, 1, 1] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 67 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237710 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237710 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237710/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237710 Building REAL300000237711 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237711' /scratch/stefan/7769818/working/building/REAL300000237711 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237711 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237711/0 /scratch/stefan/7769818/working/building/REAL300000237711 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/711 `/scratch/stefan/7769818/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1) `REAL300000237711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237711 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 130, 73, 53, 87, 87, 43, 43, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 87, 87, 201, 201, 87, 87, 43, 43, 1, 1, 1, 87, 87] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32]) total number of confs: 748 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237711 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 11, 22, 3, 1, 1, 1, 1, 1, 1, 5, 5, 31, 31, 87, 87, 87, 87, 87, 87, 1, 1, 11, 11, 1, 1, 5, 5, 87, 87, 87, 1, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 20, 21, 24, 25, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 215 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237711 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237711 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237711/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237711 Building REAL300000237712 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237712' /scratch/stefan/7769818/working/building/REAL300000237712 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237712 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237712/0 /scratch/stefan/7769818/working/building/REAL300000237712 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/712 `/scratch/stefan/7769818/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1) `REAL300000237712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237712 none O=C([O-])CCOC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 192, 189, 140, 63, 46, 81, 81, 38, 38, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 81, 81, 201, 201, 189, 189, 81, 81, 38, 38, 1, 1, 1, 81, 81] 201 rigid atoms, others: [32, 33, 12, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 735 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237712 none O=C([O-])CCOC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 26, 12, 3, 1, 1, 1, 1, 1, 1, 5, 5, 22, 22, 81, 81, 81, 81, 81, 81, 1, 1, 16, 16, 12, 12, 1, 1, 5, 5, 81, 81, 81, 1, 1] 201 rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 224 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237712 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237712 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237712/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237712 Building REAL300000237713 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237713' /scratch/stefan/7769818/working/building/REAL300000237713 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237713 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237713/0 /scratch/stefan/7769818/working/building/REAL300000237713 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/713 `/scratch/stefan/7769818/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CC(C=CC(=O)C2=CC=C(Br)N=C2)=C1)C(=O)[O-]) `REAL300000237713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237713 none CC(OC1=CC=CC(C=CC(=O)C2=CC=C(Br)N=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [186, 143, 56, 56, 56, 56, 56, 31, 31, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 56, 186, 186, 186, 186, 186, 186, 186, 56, 56, 56, 31, 31, 1, 1, 1, 56] 186 rigid atoms, others: [32, 33, 34, 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, 35]) total number of confs: 473 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237713 none CC(OC1=CC=CC(C=CC(=O)C2=CC=C(Br)N=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [30, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 56, 56, 56, 56, 56, 56, 1, 30, 44, 44, 30, 30, 30, 30, 1, 1, 1, 6, 6, 56, 56, 56, 1] 186 rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 8, 19, 27, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 235 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237713 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237713 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237713/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237713 Building REAL300000237714 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237714' /scratch/stefan/7769818/working/building/REAL300000237714 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237714 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237714/0 /scratch/stefan/7769818/working/building/REAL300000237714 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/714 `/scratch/stefan/7769818/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC(C=CC(=O)C2=CC=C(Br)N=C2)=C1) `REAL300000237714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237714 none O=C([O-])CCOC1=CC=CC(C=CC(=O)C2=CC=C(Br)N=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 192, 155, 54, 54, 54, 54, 54, 23, 23, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 54, 201, 201, 192, 192, 54, 54, 54, 23, 23, 1, 1, 1, 54] 201 rigid atoms, others: [32, 33, 34, 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, 35]) total number of confs: 470 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237714 none O=C([O-])CCOC1=CC=CC(C=CC(=O)C2=CC=C(Br)N=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 30, 44, 23, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 54, 54, 54, 54, 54, 54, 1, 30, 30, 23, 23, 1, 1, 1, 5, 5, 54, 54, 54, 1] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11, 22, 27, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 258 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237714 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237714 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237714/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237714 Building REAL300000237715 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237715' /scratch/stefan/7769818/working/building/REAL300000237715 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237715 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237715/0 /scratch/stefan/7769818/working/building/REAL300000237715 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/715 `/scratch/stefan/7769818/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C(Br)N=C3)O2)C=C1) `REAL300000237715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237715 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C(Br)N=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 12, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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: [7, 1, 7, 1, 6, 6, 1, 1, 1, 1, 1, 1, 13, 13, 50, 51, 118, 118, 118, 118, 118, 118, 1, 6, 6, 7, 6, 1, 1, 13, 13, 118, 118, 118, 6, 6] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237715 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C(Br)N=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 12, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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: [201, 118, 201, 118, 201, 201, 118, 118, 118, 118, 59, 59, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 118, 201, 201, 201, 201, 118, 118, 59, 59, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 888 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: REAL300000237715 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C(Br)N=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 12, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 44, 44, 97, 97, 164, 164, 164, 164, 164, 164, 7, 1, 1, 1, 1, 8, 7, 44, 44, 164, 164, 164, 1, 1] 164 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 373 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237715 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237715 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237715/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237715 Building REAL300000237716 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237716' /scratch/stefan/7769818/working/building/REAL300000237716 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237716 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237716/0 /scratch/stefan/7769818/working/building/REAL300000237716 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/716 `/scratch/stefan/7769818/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC(C=CC(=O)C2=CC=C(Br)N=C2)=C1) `REAL300000237716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237716 none O=C([O-])COC1=CC=CC(C=CC(=O)C2=CC=C(Br)N=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 196, 143, 62, 62, 62, 62, 62, 34, 34, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 62, 196, 196, 62, 62, 62, 34, 34, 1, 1, 1, 62] 196 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 532 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237716 none O=C([O-])COC1=CC=CC(C=CC(=O)C2=CC=C(Br)N=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [28, 20, 28, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 62, 62, 62, 62, 62, 62, 1, 20, 20, 1, 1, 1, 5, 5, 62, 62, 62, 1] 196 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 21, 24, 25, 26] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 191 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237716 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237716 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237716/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237716 Building REAL300000237717 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237717' /scratch/stefan/7769818/working/building/REAL300000237717 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237717 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237717/0 /scratch/stefan/7769818/working/building/REAL300000237717 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/717 `/scratch/stefan/7769818/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1) `REAL300000237717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237717 none O=C([O-])C(F)(F)OC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 117, 201, 201, 39, 25, 51, 51, 20, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 20, 20, 1, 1, 1, 51, 51] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 31, 32]) total number of confs: 707 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237717 none O=C([O-])C(F)(F)OC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 30, 5, 20, 20, 1, 1, 1, 1, 1, 1, 5, 5, 19, 19, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 5, 5, 51, 51, 51, 1, 1] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237717 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237717 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237717/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237717 Building REAL300000237718 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237718' /scratch/stefan/7769818/working/building/REAL300000237718 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237718 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237718/0 /scratch/stefan/7769818/working/building/REAL300000237718 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/718 `/scratch/stefan/7769818/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=CC(=O)C2=CC=C(Br)N=C2)N=N1) `REAL300000237718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237718 none O=C([O-])CN1C=C(C=CC(=O)C2=CC=C(Br)N=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 69, 69, 69, 47, 47, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 69, 69, 100, 100, 69, 47, 47, 1, 1, 1] 100 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 335 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237718 none O=C([O-])CN1C=C(C=CC(=O)C2=CC=C(Br)N=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 1, 1, 1, 1, 1, 7, 7, 22, 23, 69, 69, 69, 69, 69, 69, 1, 1, 8, 8, 1, 7, 7, 69, 69, 69] 100 rigid atoms, others: [3, 4, 5, 6, 7, 18, 19, 22] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237718 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237718 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237718/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237718 Building REAL300000237719 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237719' /scratch/stefan/7769818/working/building/REAL300000237719 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237719 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237719/0 /scratch/stefan/7769818/working/building/REAL300000237719 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/719 `/scratch/stefan/7769818/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=CC(=O)C2=CC=C(Br)N=C2)=C1) `REAL300000237719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237719 none O=C([O-])C1=CC=CC(C=CC(=O)C2=CC=C(Br)N=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 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, 7, 3, 7, 7, 7, 7, 7, 3, 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, 45, 45, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 45, 45, 1, 1, 1, 69] 69 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 28]) total number of confs: 157 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237719 none O=C([O-])C1=CC=CC(C=CC(=O)C2=CC=C(Br)N=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 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, 7, 3, 7, 7, 7, 7, 7, 3, 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, 7, 7, 39, 39, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 7, 7, 69, 69, 69, 1] 69 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 142 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237719 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237719 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237719/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237719 Building REAL300000237720 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237720' /scratch/stefan/7769818/working/building/REAL300000237720 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237720 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237720/0 /scratch/stefan/7769818/working/building/REAL300000237720 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/720 `/scratch/stefan/7769818/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(C=CC(=O)C2=CC=C(Br)N=C2)=C1) `REAL300000237720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237720 none O=C([O-])C1=CSC(C=CC(=O)C2=CC=C(Br)N=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 104, 104, 104, 50, 50, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 50, 50, 1, 1, 1, 104] 104 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 25]) total number of confs: 207 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237720 none O=C([O-])C1=CSC(C=CC(=O)C2=CC=C(Br)N=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 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, 7, 7, 7, 7, 7, 3, 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, 11, 11, 42, 42, 104, 104, 104, 104, 104, 104, 1, 1, 11, 12, 104, 104, 104, 1] 104 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237720 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237720 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237720/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237720 Building REAL300000237721 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237721' /scratch/stefan/7769818/working/building/REAL300000237721 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237721 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237721/0 /scratch/stefan/7769818/working/building/REAL300000237721 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/721 `/scratch/stefan/7769818/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C(Cl)=C1) `REAL300000237721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237721 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 69, 81, 81, 53, 53, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 53, 53, 1, 1, 1, 81] 81 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 28]) total number of confs: 244 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237721 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 52, 52, 81, 81, 81, 81, 81, 81, 1, 1, 1, 1, 1, 10, 10, 81, 81, 81, 1] 81 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27]) total number of confs: 168 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237721 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237721 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237721/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237721 Building REAL300000237722 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237722' /scratch/stefan/7769818/working/building/REAL300000237722 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237722 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237722/0 /scratch/stefan/7769818/working/building/REAL300000237722 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/722 `/scratch/stefan/7769818/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)C(C=CC(=O)C2=CC=C(Br)N=C2)=CC=C1) `REAL300000237722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237722 none O=C([O-])C1=C(Cl)C(C=CC(=O)C2=CC=C(Br)N=C2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 7, 7, 7, 7, 7, 3, 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, 125, 65, 65, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 65, 65, 1, 1, 1, 125, 125, 125] 125 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 26, 27, 28]) total number of confs: 253 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237722 none O=C([O-])C1=C(Cl)C(C=CC(=O)C2=CC=C(Br)N=C2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 7, 7, 7, 7, 7, 3, 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, 3, 1, 1, 1, 1, 1, 9, 9, 55, 55, 125, 125, 125, 125, 125, 125, 1, 1, 1, 9, 9, 125, 125, 125, 1, 1, 1] 125 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25]) total number of confs: 247 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237722 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237722 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237722/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237722 Building REAL300000237723 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237723' /scratch/stefan/7769818/working/building/REAL300000237723 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237723 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237723/0 /scratch/stefan/7769818/working/building/REAL300000237723 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/723 `/scratch/stefan/7769818/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=CC(=O)C2=CC=C(Br)N=C2)=CC=C1O) `REAL300000237723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237723 none O=C([O-])C1=CC(C=CC(=O)C2=CC=C(Br)N=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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, 115, 115, 115, 115, 64, 64, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 64, 64, 1, 1, 1, 115, 115, 230] 230 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29]) total number of confs: 462 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237723 none O=C([O-])C1=CC(C=CC(=O)C2=CC=C(Br)N=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 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: [3, 1, 3, 1, 1, 1, 1, 6, 6, 39, 39, 115, 115, 115, 115, 115, 115, 1, 1, 1, 1, 1, 6, 6, 115, 115, 115, 1, 1, 2] 230 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 29]) total number of confs: 207 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237723 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237723 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237723/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237723 Building REAL300000237724 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237724' /scratch/stefan/7769818/working/building/REAL300000237724 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237724 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237724/0 /scratch/stefan/7769818/working/building/REAL300000237724 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/724 `/scratch/stefan/7769818/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(Br)N=C1) `REAL300000237724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237724 none CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(Br)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 55, 55, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 86, 86, 86, 55, 55, 1, 1, 1] 86 rigid atoms, others: [32, 33, 34, 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]) total number of confs: 192 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237724 none CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(Br)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 59, 59, 86, 86, 86, 86, 86, 86, 2, 2, 2, 1, 2, 2, 2, 1, 9, 9, 86, 86, 86] 86 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 25, 29] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237724 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237724 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237724/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237724 Building REAL300000237725 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237725' /scratch/stefan/7769818/working/building/REAL300000237725 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237725 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237725/0 /scratch/stefan/7769818/working/building/REAL300000237725 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/725 `/scratch/stefan/7769818/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1)C(=O)[O-]) `REAL300000237725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237725 none CC(OC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 140, 66, 42, 91, 91, 42, 42, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 91, 91, 201, 201, 201, 201, 201, 201, 201, 91, 91, 42, 42, 1, 1, 1, 91, 91] 201 rigid atoms, others: [32, 33, 9, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 789 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237725 none CC(OC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 5, 5, 29, 29, 91, 91, 91, 91, 91, 91, 1, 1, 14, 19, 19, 14, 14, 14, 14, 1, 1, 5, 5, 91, 91, 91, 1, 1] 201 rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 34, 18, 19, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 213 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237725 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237725 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237725/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237725 Building REAL300000237726 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237726' /scratch/stefan/7769818/working/building/REAL300000237726 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237726 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237726/0 /scratch/stefan/7769818/working/building/REAL300000237726 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/726 `/scratch/stefan/7769818/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC=C1C=CC(=O)C1=CC=C(Br)N=C1) `REAL300000237726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237726 none O=C([O-])CCOC1=CC=CC=C1C=CC(=O)C1=CC=C(Br)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 190, 184, 128, 60, 60, 60, 46, 60, 60, 29, 29, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 201, 201, 184, 184, 60, 60, 60, 60, 29, 29, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 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]) total number of confs: 652 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237726 none O=C([O-])CCOC1=CC=CC=C1C=CC(=O)C1=CC=C(Br)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 53, 69, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 60, 60, 60, 60, 60, 60, 53, 53, 29, 29, 1, 1, 1, 1, 7, 7, 60, 60, 60] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 403 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237726 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237726 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237726/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237726 Building REAL300000237727 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237727' /scratch/stefan/7769818/working/building/REAL300000237727 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237727 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237727/0 /scratch/stefan/7769818/working/building/REAL300000237727 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/727 `/scratch/stefan/7769818/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)[O-])=C1C=CC(=O)C1=CC=C(Br)N=C1) `REAL300000237727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237727 none CN1N=CC(C(=O)[O-])=C1C=CC(=O)C1=CC=C(Br)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 51, 51, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 51, 51, 1, 1, 1] 69 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 22, 23, 24, 25]) total number of confs: 157 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237727 none CN1N=CC(C(=O)[O-])=C1C=CC(=O)C1=CC=C(Br)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 3, 3, 1, 1, 9, 9, 36, 36, 69, 69, 69, 69, 69, 69, 2, 2, 2, 1, 9, 9, 69, 69, 69] 69 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 23] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237727 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237727 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237727/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237727 Building REAL300000237728 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237728' /scratch/stefan/7769818/working/building/REAL300000237728 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237728 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237728/0 /scratch/stefan/7769818/working/building/REAL300000237728 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/728 `/scratch/stefan/7769818/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1F) `REAL300000237728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237728 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 120, 120, 120, 71, 71, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 120, 71, 71, 1, 1, 1, 120] 120 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 28]) total number of confs: 252 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237728 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 44, 44, 120, 120, 120, 120, 120, 120, 1, 1, 1, 1, 1, 6, 6, 120, 120, 120, 1] 120 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27]) total number of confs: 215 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237728 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237728 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237728/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237728 Building REAL300000237729 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237729' /scratch/stefan/7769818/working/building/REAL300000237729 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237729 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237729/0 /scratch/stefan/7769818/working/building/REAL300000237729 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/729 `/scratch/stefan/7769818/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)O1) `REAL300000237729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237729 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 12, 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, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 172, 121, 121, 121, 121, 62, 62, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 121, 172, 172, 121, 121, 62, 62, 1, 1, 1] 172 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 427 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237729 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 12, 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, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [20, 10, 21, 10, 1, 1, 1, 1, 1, 1, 12, 12, 42, 42, 121, 121, 121, 121, 121, 121, 1, 11, 10, 1, 1, 12, 12, 121, 121, 121] 172 rigid atoms, others: [4, 5, 6, 7, 8, 9, 20, 23, 24] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237729 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237729 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237729/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237729 Building REAL300000237730 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237730' /scratch/stefan/7769818/working/building/REAL300000237730 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237730 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237730/0 /scratch/stefan/7769818/working/building/REAL300000237730 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/730 `/scratch/stefan/7769818/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1C(=O)[O-]) `REAL300000237730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237730 none COC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1C(=O)[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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 7, 3, 7, 7, 7, 7, 7, 3, 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, 115, 115, 115, 115, 57, 57, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 201, 201, 201, 201, 201, 115, 115, 57, 57, 1, 1, 1, 115] 201 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 749 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237730 none COC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1C(=O)[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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 7, 3, 7, 7, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 5, 5, 38, 38, 115, 115, 115, 115, 115, 115, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 5, 5, 115, 115, 115, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 17, 18, 19, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 202 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237730 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237730 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237730/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237730 Building REAL300000237731 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237731' /scratch/stefan/7769818/working/building/REAL300000237731 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237731 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237731/0 /scratch/stefan/7769818/working/building/REAL300000237731 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/731 `/scratch/stefan/7769818/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=CC=C(Br)N=C2)=C1) `REAL300000237731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237731 none O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=CC=C(Br)N=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 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, 7, 7, 7, 7, 7, 3, 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, 111, 65, 65, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 65, 65, 1, 1, 1, 108] 111 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 22, 23, 24, 28]) total number of confs: 232 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237731 none O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=CC=C(Br)N=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 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, 7, 7, 7, 7, 7, 3, 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, 1, 11, 11, 67, 67, 111, 111, 111, 111, 111, 111, 1, 1, 1, 11, 11, 111, 111, 111, 1] 111 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 233 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237731 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237731 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237731/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237731 Building REAL300000237732 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237732' /scratch/stefan/7769818/working/building/REAL300000237732 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237732 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237732/0 /scratch/stefan/7769818/working/building/REAL300000237732 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/732 `/scratch/stefan/7769818/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(Br)N=C1) `REAL300000237732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237732 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(Br)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.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, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 92, 92, 92, 92, 92, 137, 92, 92, 139, 139, 92, 34, 34, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 92, 137, 137, 137, 92, 34, 34, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 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]) total number of confs: 530 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237732 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(Br)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.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, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 1, 1, 3, 3, 1, 1, 1, 9, 9, 46, 46, 92, 92, 92, 92, 92, 92, 4, 4, 4, 1, 3, 3, 3, 1, 9, 9, 92, 92, 92] 201 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 11, 12, 13, 27, 31] set([0, 6, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237732 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237732 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237732/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237732 Building REAL300000237733 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237733' /scratch/stefan/7769818/working/building/REAL300000237733 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237733 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237733/0 /scratch/stefan/7769818/working/building/REAL300000237733 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/733 `/scratch/stefan/7769818/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=CC(=O)C2=CC=C(Br)N=C2)=CC=C1F) `REAL300000237733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237733 none O=C([O-])C1=CC(C=CC(=O)C2=CC=C(Br)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 68, 68, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 68, 68, 1, 1, 1, 131, 131] 131 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 266 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237733 none O=C([O-])C1=CC(C=CC(=O)C2=CC=C(Br)N=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 6, 6, 41, 41, 131, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 6, 6, 131, 131, 131, 1, 1] 131 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26]) total number of confs: 223 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237733 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237733 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237733/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237733 Building REAL300000237734 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237734' /scratch/stefan/7769818/working/building/REAL300000237734 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237734 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237734/0 /scratch/stefan/7769818/working/building/REAL300000237734 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/734 `/scratch/stefan/7769818/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1) `REAL300000237734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237734 none O=C([O-])CC1=CC=C(C=CC(=O)C2=CC=C(Br)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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 7, 7, 7, 7, 7, 3, 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, 69, 78, 78, 53, 53, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 78, 53, 53, 1, 1, 1, 78, 78] 78 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 219 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237734 none O=C([O-])CC1=CC=C(C=CC(=O)C2=CC=C(Br)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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 7, 7, 7, 7, 7, 3, 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: [4, 2, 4, 1, 1, 1, 1, 1, 1, 6, 6, 35, 35, 78, 78, 78, 78, 78, 78, 1, 1, 2, 2, 1, 1, 6, 6, 78, 78, 78, 1, 1] 78 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: 161 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237734 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237734 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237734/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237734 Building REAL300000237735 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237735' /scratch/stefan/7769818/working/building/REAL300000237735 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237735 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237735/0 /scratch/stefan/7769818/working/building/REAL300000237735 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/735 `/scratch/stefan/7769818/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)S1) `REAL300000237735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237735 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 75, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 33, 33, 1, 1, 1] 75 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237735 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 2, 1, 1, 1, 1, 1, 11, 11, 39, 39, 75, 75, 75, 75, 75, 75, 1, 1, 1, 11, 11, 75, 75, 75] 75 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237735 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237735 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237735/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237735 Building REAL300000237736 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237736' /scratch/stefan/7769818/working/building/REAL300000237736 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237736 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237736/0 /scratch/stefan/7769818/working/building/REAL300000237736 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/736 `/scratch/stefan/7769818/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1) `REAL300000237736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237736 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 113, 76, 129, 129, 76, 75, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 129, 129, 75, 76, 1, 1, 1, 129, 129] 129 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32]) total number of confs: 533 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237736 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [12, 3, 12, 3, 1, 1, 1, 1, 1, 1, 5, 5, 45, 45, 129, 129, 129, 129, 129, 129, 1, 1, 3, 3, 1, 1, 5, 5, 129, 129, 129, 1, 1] 129 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 20, 21, 24, 25, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 249 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237736 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237736 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237736/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237736 Building REAL300000237737 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237737' /scratch/stefan/7769818/working/building/REAL300000237737 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237737 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237737/0 /scratch/stefan/7769818/working/building/REAL300000237737 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/737 `/scratch/stefan/7769818/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CC=C(Br)N=C2)C(F)=C1) `REAL300000237737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237737 none O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CC=C(Br)N=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 192, 192, 192, 192, 192, 81, 81, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 192, 192, 192, 192, 81, 81, 1, 1, 1, 192] 192 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 28]) total number of confs: 342 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237737 none O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CC=C(Br)N=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 95, 95, 192, 192, 192, 192, 192, 192, 1, 1, 1, 1, 11, 11, 192, 192, 192, 1] 192 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 373 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237737 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237737 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237737/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237737 Building REAL300000237738 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237738' /scratch/stefan/7769818/working/building/REAL300000237738 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237738 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237738/0 /scratch/stefan/7769818/working/building/REAL300000237738 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/738 `/scratch/stefan/7769818/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NNC2=CC=CC(C=CC(=O)C3=CC=C(Br)N=C3)=C21) `REAL300000237738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237738 none O=C([O-])C1=NNC2=CC=CC(C=CC(=O)C3=CC=C(Br)N=C3)=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 79, 79, 79, 52, 52, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 52, 52, 1, 1, 1] 79 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 177 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237738 none O=C([O-])C1=NNC2=CC=CC(C=CC(=O)C3=CC=C(Br)N=C3)=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 44, 44, 79, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 9, 9, 79, 79, 79] 79 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237738 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237738 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237738/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237738 Building REAL300000237739 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237739' /scratch/stefan/7769818/working/building/REAL300000237739 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237739 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237739/0 /scratch/stefan/7769818/working/building/REAL300000237739 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/739 `/scratch/stefan/7769818/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2NC=C(C=CC(=O)C3=CC=C(Br)N=C3)C2=C1) `REAL300000237739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237739 none O=C([O-])C1=CC=C2NC=C(C=CC(=O)C3=CC=C(Br)N=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 104, 104, 104, 104, 104, 104, 48, 48, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 104, 104, 48, 48, 1, 1, 1, 104] 104 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 198 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237739 none O=C([O-])C1=CC=C2NC=C(C=CC(=O)C3=CC=C(Br)N=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 11, 59, 59, 104, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 1, 11, 11, 104, 104, 104, 1] 104 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 21, 22, 23, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237739 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237739 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237739/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237739 Building REAL300000237740 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237740' /scratch/stefan/7769818/working/building/REAL300000237740 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237740 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237740/0 /scratch/stefan/7769818/working/building/REAL300000237740 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/740 `/scratch/stefan/7769818/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=N1) `REAL300000237740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237740 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 44, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 44, 44, 1, 1, 1, 60] 60 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 27]) total number of confs: 139 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237740 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 33, 33, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1, 6, 6, 60, 60, 60, 1] 60 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237740 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237740 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237740/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237740 Building REAL300000237741 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237741' /scratch/stefan/7769818/working/building/REAL300000237741 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237741 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237741/0 /scratch/stefan/7769818/working/building/REAL300000237741 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/741 `/scratch/stefan/7769818/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1O) `REAL300000237741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237741 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 236 conformations in input total number of sets (complete confs): 236 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 118, 118, 71, 71, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 118, 71, 71, 1, 1, 1, 117, 236] 236 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 490 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237741 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 236 conformations in input total number of sets (complete confs): 236 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 42, 42, 118, 117, 118, 118, 118, 118, 1, 1, 1, 1, 1, 6, 6, 118, 118, 118, 1, 2] 236 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 29]) total number of confs: 212 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237741 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237741 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237741/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237741 Building REAL300000237742 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237742' /scratch/stefan/7769818/working/building/REAL300000237742 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237742 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237742/0 /scratch/stefan/7769818/working/building/REAL300000237742 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/742 `/scratch/stefan/7769818/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1C(=O)[O-]) `REAL300000237742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237742 none CC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [143, 143, 143, 143, 73, 73, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 73, 73, 1, 1, 1, 143] 143 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 291 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237742 none CC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 41, 41, 143, 143, 143, 143, 143, 143, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 6, 6, 143, 143, 143, 1] 143 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 245 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237742 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237742 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237742/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237742 Building REAL300000237743 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237743' /scratch/stefan/7769818/working/building/REAL300000237743 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237743 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237743/0 /scratch/stefan/7769818/working/building/REAL300000237743 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/743 `/scratch/stefan/7769818/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)SC(C=CC(=O)C2=CC=C(Br)N=C2)=C1) `REAL300000237743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237743 none O=C([O-])C1=C(Cl)SC(C=CC(=O)C2=CC=C(Br)N=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 64, 64, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 201, 64, 64, 1, 1, 1, 201] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 25]) total number of confs: 326 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237743 none O=C([O-])C1=C(Cl)SC(C=CC(=O)C2=CC=C(Br)N=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 93, 94, 201, 201, 201, 201, 201, 201, 1, 13, 13, 201, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24]) total number of confs: 392 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237743 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237743 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237743/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237743 Building REAL300000237744 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237744' /scratch/stefan/7769818/working/building/REAL300000237744 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237744 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237744/0 /scratch/stefan/7769818/working/building/REAL300000237744 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/744 `/scratch/stefan/7769818/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CC=C(Br)N=C2)O1) `REAL300000237744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237744 none CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CC=C(Br)N=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 12, 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, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 158, 158, 158, 158, 65, 65, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 158, 65, 65, 1, 1, 1] 158 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237744 none CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CC=C(Br)N=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 12, 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, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 12, 12, 85, 85, 158, 158, 158, 158, 158, 158, 1, 2, 2, 2, 1, 12, 12, 158, 158, 158] 158 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 19, 23] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237744 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237744 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237744/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237744 Building REAL300000237745 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237745' /scratch/stefan/7769818/working/building/REAL300000237745 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237745 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237745/0 /scratch/stefan/7769818/working/building/REAL300000237745 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/745 `/scratch/stefan/7769818/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(Br)N=C1) `REAL300000237745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237745 none CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(Br)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 80, 80, 80, 80, 45, 45, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 45, 45, 1, 1, 1] 80 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 22, 23, 24, 25]) total number of confs: 170 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237745 none CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(Br)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 45, 45, 80, 80, 80, 80, 80, 80, 2, 2, 2, 1, 10, 10, 80, 80, 80] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237745 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237745 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237745/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237745 Building REAL300000237746 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237746' /scratch/stefan/7769818/working/building/REAL300000237746 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237746 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237746/0 /scratch/stefan/7769818/working/building/REAL300000237746 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/746 `/scratch/stefan/7769818/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=CC(C=CC(=O)C2=CC=C(Br)N=C2)=C1) `REAL300000237746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237746 none O=C([O-])C1=CN=CC(C=CC(=O)C2=CC=C(Br)N=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 68, 68, 68, 68, 44, 44, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 44, 44, 1, 1, 1, 68] 68 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 27]) total number of confs: 155 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237746 none O=C([O-])C1=CN=CC(C=CC(=O)C2=CC=C(Br)N=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 39, 39, 68, 68, 68, 68, 68, 68, 1, 1, 1, 7, 7, 68, 68, 68, 1] 68 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26]) total number of confs: 140 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237746 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237746 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237746/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237746 Building REAL300000237747 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237747' /scratch/stefan/7769818/working/building/REAL300000237747 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237747 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237747/0 /scratch/stefan/7769818/working/building/REAL300000237747 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/747 `/scratch/stefan/7769818/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=COC(C=CC(=O)C2=CC=C(Br)N=C2)=C1) `REAL300000237747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237747 none O=C([O-])C1=COC(C=CC(=O)C2=CC=C(Br)N=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 49, 49, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 49, 49, 1, 1, 1, 73] 73 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 25]) total number of confs: 158 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237747 none O=C([O-])C1=COC(C=CC(=O)C2=CC=C(Br)N=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 11, 11, 34, 34, 73, 73, 73, 73, 73, 73, 1, 1, 11, 11, 73, 73, 73, 1] 73 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237747 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237747 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237747/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237747 Building REAL300000237748 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237748' /scratch/stefan/7769818/working/building/REAL300000237748 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237748 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237748/0 /scratch/stefan/7769818/working/building/REAL300000237748 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/748 `/scratch/stefan/7769818/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(Br)N=C1) `REAL300000237748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237748 none COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(Br)N=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', '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, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 93, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 93, 93, 1, 1, 1] 201 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 368 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237748 none COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C(Br)N=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', '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, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 89, 89, 201, 201, 201, 201, 201, 201, 4, 4, 4, 1, 1, 1, 9, 9, 201, 201, 201] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27] set([0, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 388 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237748 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237748 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237748/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237748 Building REAL300000237749 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237749' /scratch/stefan/7769818/working/building/REAL300000237749 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237749 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237749/0 /scratch/stefan/7769818/working/building/REAL300000237749 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/749 `/scratch/stefan/7769818/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2SC=C(C=CC(=O)C3=CC=C(Br)N=C3)C2=C1) `REAL300000237749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237749 none O=C([O-])C1=CC=C2SC=C(C=CC(=O)C3=CC=C(Br)N=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 79, 79, 41, 41, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 41, 41, 1, 1, 1, 79] 79 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237749 none O=C([O-])C1=CC=C2SC=C(C=CC(=O)C3=CC=C(Br)N=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 47, 47, 79, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 9, 9, 79, 79, 79, 1] 79 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237749 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237749 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237749/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237749 Building REAL300000237750 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237750' /scratch/stefan/7769818/working/building/REAL300000237750 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237750 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237750/0 /scratch/stefan/7769818/working/building/REAL300000237750 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/750 `/scratch/stefan/7769818/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C([N+](=O)[O-])=C1) `REAL300000237750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237750 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 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, 61, 65, 65, 51, 51, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 51, 51, 1, 1, 1, 65] 65 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237750 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 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, 5, 5, 43, 43, 65, 65, 65, 65, 65, 65, 1, 1, 2, 2, 1, 1, 1, 5, 5, 65, 65, 65, 1] 65 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 22, 23, 24, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237750 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237750 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237750/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237750 Building REAL300000237751 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237751' /scratch/stefan/7769818/working/building/REAL300000237751 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237751 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237751/0 /scratch/stefan/7769818/working/building/REAL300000237751 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/751 `/scratch/stefan/7769818/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C=CC(=O)C2=CC=C(Br)N=C2)=C1) `REAL300000237751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237751 none O=C([O-])CC1=CC=CC(C=CC(=O)C2=CC=C(Br)N=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 128, 128, 107, 128, 128, 74, 74, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 128, 176, 176, 108, 128, 128, 74, 74, 1, 1, 1, 128] 176 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 615 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237751 none O=C([O-])CC1=CC=CC(C=CC(=O)C2=CC=C(Br)N=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 41, 41, 128, 128, 128, 128, 128, 128, 1, 2, 2, 1, 1, 1, 5, 5, 128, 128, 128, 1] 176 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 20, 23, 24, 25, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 228 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237751 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237751 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237751/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237751 Building REAL300000237752 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237752' /scratch/stefan/7769818/working/building/REAL300000237752 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237752 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237752/0 /scratch/stefan/7769818/working/building/REAL300000237752 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/752 `/scratch/stefan/7769818/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CC=C(Br)N=C2)=CC=C1C(=O)[O-]) `REAL300000237752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237752 none COC1=CC(C=CC(=O)C2=CC=C(Br)N=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 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, 7, 7, 7, 7, 7, 3, 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, 141, 141, 141, 60, 60, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 201, 201, 201, 201, 201, 141, 60, 60, 1, 1, 1, 141, 141] 201 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32]) total number of confs: 639 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237752 none COC1=CC(C=CC(=O)C2=CC=C(Br)N=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 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, 7, 7, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 5, 5, 38, 38, 141, 141, 141, 141, 141, 141, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 5, 5, 141, 141, 141, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 16, 17, 18, 19, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 227 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237752 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237752 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237752/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237752 Building REAL300000237753 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237753' /scratch/stefan/7769818/working/building/REAL300000237753 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237753 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237753/0 /scratch/stefan/7769818/working/building/REAL300000237753 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/753 `/scratch/stefan/7769818/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CC=C(Br)N=C2)C(F)=C1) `REAL300000237753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237753 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CC=C(Br)N=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 46, 46, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 46, 46, 1, 1, 1, 53] 53 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 28]) total number of confs: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237753 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CC=C(Br)N=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 33, 33, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 6, 6, 51, 51, 51, 1] 51 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237753 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237753 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237753/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237753 Building REAL300000237754 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237754' /scratch/stefan/7769818/working/building/REAL300000237754 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237754 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237754/0 /scratch/stefan/7769818/working/building/REAL300000237754 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/754 `/scratch/stefan/7769818/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=C(Br)N=C2)=C(F)C=C1) `REAL300000237754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237754 none O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=C(Br)N=C2)=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 75, 75, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 75, 75, 1, 1, 1, 201, 201] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237754 none O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=C(Br)N=C2)=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 11, 11, 95, 95, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 11, 11, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237754 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237754 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237754/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237754 Building REAL300000237755 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237755' /scratch/stefan/7769818/working/building/REAL300000237755 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237755 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237755/0 /scratch/stefan/7769818/working/building/REAL300000237755 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/755 `/scratch/stefan/7769818/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=CC(=O)C2=CC=C(Br)N=C2)=CS1) `REAL300000237755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237755 none O=C([O-])C1=CC(C=CC(=O)C2=CC=C(Br)N=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 41, 41, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 41, 41, 1, 1, 1, 67] 67 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 25]) total number of confs: 144 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237755 none O=C([O-])C1=CC(C=CC(=O)C2=CC=C(Br)N=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 6, 6, 31, 31, 67, 67, 67, 67, 67, 67, 1, 1, 1, 6, 6, 67, 67, 67, 1] 67 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237755 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237755 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237755/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237755 Building REAL300000237756 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237756' /scratch/stefan/7769818/working/building/REAL300000237756 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237756 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237756/0 /scratch/stefan/7769818/working/building/REAL300000237756 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/756 `/scratch/stefan/7769818/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1F) `REAL300000237756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237756 none O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 57, 69, 69, 69, 57, 57, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 57, 57, 1, 1, 1, 69] 69 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 28]) total number of confs: 223 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237756 none O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 3, 1, 1, 1, 1, 1, 1, 4, 4, 26, 26, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 4, 4, 69, 69, 69, 1] 69 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 127 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237756 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237756 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237756/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237756 Building REAL300000237757 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237757' /scratch/stefan/7769818/working/building/REAL300000237757 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237757 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237757/0 /scratch/stefan/7769818/working/building/REAL300000237757 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/757 `/scratch/stefan/7769818/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=C(C=CC(=O)C3=CC=C(Br)N=C3)O2)N1) `REAL300000237757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237757 none O=C([O-])C1=CC2=C(C=C(C=CC(=O)C3=CC=C(Br)N=C3)O2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 4, 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, 34, 34, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 34, 34, 1, 1, 1, 63] 63 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237757 none O=C([O-])C1=CC2=C(C=C(C=CC(=O)C3=CC=C(Br)N=C3)O2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 38, 38, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 12, 12, 63, 63, 63, 1] 63 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237757 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237757 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237757/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237757 Building REAL300000237758 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237758' /scratch/stefan/7769818/working/building/REAL300000237758 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237758 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237758/0 /scratch/stefan/7769818/working/building/REAL300000237758 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/758 `/scratch/stefan/7769818/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC(C=CC(=O)C3=CC=C(Br)N=C3)=CC=C2O1) `REAL300000237758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237758 none O=C([O-])C1=CC2=CC(C=CC(=O)C3=CC=C(Br)N=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 68, 68, 68, 68, 53, 53, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 68, 68, 53, 53, 1, 1, 1, 68, 68] 68 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 159 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237758 none O=C([O-])C1=CC2=CC(C=CC(=O)C3=CC=C(Br)N=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 36, 36, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 6, 6, 68, 68, 68, 1, 1] 68 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29]) total number of confs: 148 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237758 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237758 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237758/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237758 Building REAL300000237759 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237759' /scratch/stefan/7769818/working/building/REAL300000237759 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237759 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237759/0 /scratch/stefan/7769818/working/building/REAL300000237759 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/759 `/scratch/stefan/7769818/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2C(C=CC(=O)C3=CC=C(Br)N=C3)=CC=CN12) `REAL300000237759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237759 none O=C([O-])C1=CN=C2C(C=CC(=O)C3=CC=C(Br)N=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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, 94, 94, 51, 51, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 94, 51, 51, 1, 1, 1, 94, 94, 94] 94 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237759 none O=C([O-])C1=CN=C2C(C=CC(=O)C3=CC=C(Br)N=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 60, 60, 94, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 11, 11, 94, 94, 94, 1, 1, 1] 94 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237759 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237759 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237759/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237759 Building REAL300000237760 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237760' /scratch/stefan/7769818/working/building/REAL300000237760 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237760 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237760/0 /scratch/stefan/7769818/working/building/REAL300000237760 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/760 `/scratch/stefan/7769818/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CC=C(Br)N=C1) `REAL300000237760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237760 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CC=C(Br)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.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, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88, 55, 55, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 88, 88, 88, 55, 55, 1, 1, 1] 88 rigid atoms, others: [34, 35, 36, 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]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237760 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CC=C(Br)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.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, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 55, 56, 88, 88, 88, 88, 88, 88, 2, 2, 2, 1, 1, 1, 1, 10, 10, 88, 88, 88] 88 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([32, 33, 34, 35, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237760 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237760 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237760/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237760 Building REAL300000237761 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237761' /scratch/stefan/7769818/working/building/REAL300000237761 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237761 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237761/0 /scratch/stefan/7769818/working/building/REAL300000237761 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/761 `/scratch/stefan/7769818/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN2C(C=CC(=O)C3=CC=C(Br)N=C3)=CN=C2C=C1) `REAL300000237761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237761 none O=C([O-])C1=CN2C(C=CC(=O)C3=CC=C(Br)N=C3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 8, 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, 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 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 112, 112, 112, 51, 51, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 112, 112, 112, 112, 112, 112, 51, 51, 1, 1, 1, 112, 112, 112] 112 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 213 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237761 none O=C([O-])C1=CN2C(C=CC(=O)C3=CC=C(Br)N=C3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 8, 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, 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 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 12, 67, 67, 112, 112, 112, 112, 112, 112, 1, 1, 1, 1, 1, 1, 12, 12, 112, 112, 112, 1, 1, 1] 112 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237761 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237761 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237761/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237761 Building REAL300000237762 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237762' /scratch/stefan/7769818/working/building/REAL300000237762 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237762 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237762/0 /scratch/stefan/7769818/working/building/REAL300000237762 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/762 `/scratch/stefan/7769818/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=CC=C(Br)N=C3)C=C2)C=N1) `REAL300000237762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237762 none O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=CC=C(Br)N=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 40, 40, 103, 103, 103, 103, 103, 103, 1, 1, 6, 6, 6, 1, 1, 5, 5, 103, 103, 103, 1, 1, 6] 111 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 21, 22, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 35]) total number of confs: 192 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237762 none O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=CC=C(Br)N=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 103, 84, 103, 103, 55, 55, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 103, 103, 111, 111, 111, 103, 103, 55, 55, 1, 1, 1, 103, 103, 111] 111 rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 320 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: REAL300000237762 none O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=CC=C(Br)N=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 6, 6, 1, 5, 16, 16, 71, 71, 111, 111, 111, 111, 111, 111, 6, 6, 1, 1, 1, 6, 6, 16, 16, 111, 111, 111, 6, 6, 1] 111 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 23, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 265 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237762 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237762 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237762/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237762 Building REAL300000237763 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237763' /scratch/stefan/7769818/working/building/REAL300000237763 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237763 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237763/0 /scratch/stefan/7769818/working/building/REAL300000237763 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/763 `/scratch/stefan/7769818/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=C(Br)N=C2)=CC=C1) `REAL300000237763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237763 none O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=C(Br)N=C2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 187, 187, 187, 187, 73, 73, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 187, 187, 187, 73, 73, 1, 1, 1, 187, 187, 187] 187 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 26, 27, 28]) total number of confs: 328 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237763 none O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=C(Br)N=C2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 11, 11, 83, 83, 187, 187, 187, 187, 187, 187, 1, 1, 1, 11, 11, 187, 187, 187, 1, 1, 1] 187 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25]) total number of confs: 362 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237763 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237763 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237763/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237763 Building REAL300000237764 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237764' /scratch/stefan/7769818/working/building/REAL300000237764 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237764 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237764/0 /scratch/stefan/7769818/working/building/REAL300000237764 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/764 `/scratch/stefan/7769818/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1Cl) `REAL300000237764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237764 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 153, 70, 51, 70, 70, 31, 31, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 201, 201, 70, 70, 31, 31, 1, 1, 1, 70] 201 rigid atoms, others: [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, 32]) total number of confs: 616 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237764 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=C(Br)N=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 28, 46, 7, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 70, 70, 70, 70, 70, 70, 1, 1, 1, 28, 28, 1, 1, 5, 5, 70, 70, 70, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 262 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237764 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237764 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237764/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237764 Building REAL300000237765 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237765' /scratch/stefan/7769818/working/building/REAL300000237765 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237765 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237765/0 /scratch/stefan/7769818/working/building/REAL300000237765 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/765 `/scratch/stefan/7769818/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC=C(Br)N=C1) `REAL300000237765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237765 none COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC=C(Br)N=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', '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, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 153, 153, 153, 153, 153, 153, 153, 81, 81, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 153, 153, 81, 81, 1, 1, 1] 153 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 302 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237765 none COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC=C(Br)N=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', '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, 1, 1, 1, 11, 1, 1, 1, 1, 17, 8, 1, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 72, 72, 153, 153, 153, 153, 153, 153, 3, 3, 3, 1, 1, 1, 11, 11, 153, 153, 153] 153 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27] set([0, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 296 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237765 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237765 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237765/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237765 Building REAL300000237766 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237766' /scratch/stefan/7769818/working/building/REAL300000237766 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237766 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237766/0 /scratch/stefan/7769818/working/building/REAL300000237766 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/766 `/scratch/stefan/7769818/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1OCC(=O)[O-]) `REAL300000237766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237766 none COC1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 12, 5, 1, 11, 11, 7, 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, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 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: [77, 42, 42, 42, 16, 16, 10, 1, 10, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 42, 42, 42, 42, 130, 201, 201, 201, 77, 77, 77, 42, 16, 16, 1, 1, 1, 42, 42, 201, 201] 201 rigid atoms, others: [33, 34, 35, 7, 9, 10, 11, 12, 13, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 647 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237766 none COC1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 12, 5, 1, 11, 11, 7, 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, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 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, 13, 13, 42, 42, 22, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 9, 28, 34, 34, 3, 3, 3, 1, 5, 5, 42, 42, 42, 1, 1, 28, 28] 201 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 36, 30, 37] set([0, 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, 38, 39]) total number of confs: 259 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237766 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237766 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237766/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237766 Building REAL300000237767 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237767' /scratch/stefan/7769818/working/building/REAL300000237767 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237767 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237767/0 /scratch/stefan/7769818/working/building/REAL300000237767 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/767 `/scratch/stefan/7769818/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1) `REAL300000237767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237767 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 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, 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 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, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 37, 37, 37, 37, 37, 37, 1, 1, 1, 37, 37] 37 rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 103 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237767 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 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, 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 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, 3, 3, 19, 19, 37, 37, 27, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 3, 3, 37, 37, 37, 1, 1] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237767 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237767 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237767/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237767 Building REAL300000237768 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237768' /scratch/stefan/7769818/working/building/REAL300000237768 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237768 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237768/0 /scratch/stefan/7769818/working/building/REAL300000237768 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/768 `/scratch/stefan/7769818/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1) `REAL300000237768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237768 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 145, 39, 39, 96, 96, 39, 39, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 96, 96, 201, 201, 96, 96, 39, 39, 1, 1, 1, 96, 96] 201 rigid atoms, others: [32, 33, 11, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 752 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237768 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 11, 22, 3, 1, 1, 1, 1, 1, 1, 5, 5, 34, 34, 96, 96, 39, 96, 96, 96, 96, 96, 96, 1, 1, 11, 11, 1, 1, 5, 5, 96, 96, 96, 1, 1] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 23, 24, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 379 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237768 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237768 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237768/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237768 Building REAL300000237769 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237769' /scratch/stefan/7769818/working/building/REAL300000237769 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237769 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237769/0 /scratch/stefan/7769818/working/building/REAL300000237769 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/769 `/scratch/stefan/7769818/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1) `REAL300000237769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237769 none O=C([O-])CCOC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 195, 152, 34, 34, 89, 89, 34, 34, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 89, 89, 201, 201, 195, 195, 89, 89, 34, 34, 1, 1, 1, 89, 89] 201 rigid atoms, others: [34, 35, 36, 12, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 689 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237769 none O=C([O-])CCOC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 14, 19, 11, 3, 1, 1, 1, 1, 1, 1, 5, 5, 39, 39, 89, 89, 40, 89, 89, 89, 89, 89, 89, 1, 1, 13, 13, 11, 11, 1, 1, 5, 5, 89, 89, 89, 1, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 24, 25, 38, 37, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 360 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237769 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237769 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237769/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237769 Building REAL300000237770 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237770' /scratch/stefan/7769818/working/building/REAL300000237770 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237770 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237770/0 /scratch/stefan/7769818/working/building/REAL300000237770 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/770 `/scratch/stefan/7769818/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1)C(=O)[O-]) `REAL300000237770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237770 none CC(OC1=CC=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 169, 60, 60, 60, 60, 60, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 60, 201, 201, 201, 201, 201, 201, 201, 60, 60, 60, 33, 33, 1, 1, 1, 60] 201 rigid atoms, others: [35, 36, 37, 10, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 476 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237770 none CC(OC1=CC=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 1, 5, 5, 20, 20, 60, 60, 36, 60, 60, 60, 60, 60, 60, 1, 24, 34, 34, 24, 24, 24, 24, 1, 1, 1, 5, 5, 60, 60, 60, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 22, 38, 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]) total number of confs: 300 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237770 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237770 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237770/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237770 Building REAL300000237771 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237771' /scratch/stefan/7769818/working/building/REAL300000237771 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237771 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237771/0 /scratch/stefan/7769818/working/building/REAL300000237771 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/771 `/scratch/stefan/7769818/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1) `REAL300000237771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237771 none O=C([O-])CCOC1=CC=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 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, 165, 62, 62, 62, 62, 62, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 62, 201, 201, 199, 199, 62, 62, 62, 23, 23, 1, 1, 1, 62] 201 rigid atoms, others: [35, 36, 37, 13, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 470 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237771 none O=C([O-])CCOC1=CC=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 25, 38, 23, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 62, 62, 30, 62, 62, 62, 62, 62, 62, 1, 25, 25, 23, 23, 1, 1, 1, 6, 6, 62, 62, 62, 1] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 25, 38, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 333 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237771 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237771 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237771/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237771 Building REAL300000237772 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237772' /scratch/stefan/7769818/working/building/REAL300000237772 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237772 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237772/0 /scratch/stefan/7769818/working/building/REAL300000237772 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/772 `/scratch/stefan/7769818/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)O2)C=C1) `REAL300000237772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237772 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 12, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 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: [7, 1, 7, 1, 6, 6, 1, 1, 1, 1, 1, 1, 12, 12, 54, 54, 129, 129, 84, 129, 129, 129, 129, 129, 129, 1, 6, 6, 6, 6, 1, 1, 12, 12, 129, 129, 129, 6, 6] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 417 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237772 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 12, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 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: [201, 129, 201, 129, 201, 201, 129, 129, 129, 129, 57, 57, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 129, 201, 201, 201, 201, 129, 129, 57, 57, 1, 1, 1, 201, 201] 201 rigid atoms, others: [34, 35, 36, 13, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 827 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: REAL300000237772 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 12, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 45, 45, 129, 129, 201, 201, 178, 201, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 7, 7, 45, 45, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 26, 27, 28, 29, 37] set([0, 2, 8, 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: 558 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237772 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237772 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237772/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237772 Building REAL300000237773 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237773' /scratch/stefan/7769818/working/building/REAL300000237773 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237773 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237773/0 /scratch/stefan/7769818/working/building/REAL300000237773 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/773 `/scratch/stefan/7769818/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1) `REAL300000237773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237773 none O=C([O-])COC1=CC=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 157, 67, 67, 67, 67, 67, 39, 39, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 67, 201, 201, 67, 67, 67, 39, 39, 1, 1, 1, 67] 201 rigid atoms, others: [32, 33, 34, 12, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 544 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237773 none O=C([O-])COC1=CC=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 19, 31, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 67, 67, 24, 67, 67, 67, 67, 67, 67, 1, 19, 19, 1, 1, 1, 6, 6, 67, 67, 67, 1] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 24, 27, 28, 29] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 321 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237773 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237773 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237773/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237773 Building REAL300000237774 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237774' /scratch/stefan/7769818/working/building/REAL300000237774 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237774 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237774/0 /scratch/stefan/7769818/working/building/REAL300000237774 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/774 `/scratch/stefan/7769818/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1) `REAL300000237774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237774 none O=C([O-])C(F)(F)OC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 15, 15, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 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, 130, 201, 201, 33, 33, 53, 53, 19, 19, 11, 1, 11, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 53, 53, 53, 53, 19, 19, 1, 1, 1, 53, 53] 201 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 654 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237774 none O=C([O-])C(F)(F)OC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 15, 15, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 25, 36, 7, 25, 25, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 53, 53, 24, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 5, 5, 53, 53, 53, 1, 1] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33]) total number of confs: 287 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237774 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237774 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237774/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237774 Building REAL300000237775 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237775' /scratch/stefan/7769818/working/building/REAL300000237775 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237775 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237775/0 /scratch/stefan/7769818/working/building/REAL300000237775 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/775 `/scratch/stefan/7769818/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1) `REAL300000237775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237775 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 70, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 201, 201, 201, 201, 70, 70, 1, 1, 1, 201, 201] 201 rigid atoms, others: [34, 35, 36, 14, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 335 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237775 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 9, 9, 71, 71, 201, 201, 115, 201, 201, 201, 201, 201, 201, 1, 1, 3, 3, 3, 1, 9, 9, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 38, 9, 10, 11, 12, 26, 27, 37, 31] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 630 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237775 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237775 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237775/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237775 Building REAL300000237776 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237776' /scratch/stefan/7769818/working/building/REAL300000237776 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237776 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237776/0 /scratch/stefan/7769818/working/building/REAL300000237776 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/776 `/scratch/stefan/7769818/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)N=N1) `REAL300000237776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237776 none O=C([O-])CN1C=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 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, 71, 71, 71, 39, 39, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 71, 71, 106, 106, 71, 39, 39, 1, 1, 1] 106 rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 346 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237776 none O=C([O-])CN1C=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 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: [14, 8, 14, 1, 1, 1, 1, 1, 11, 11, 30, 31, 71, 71, 56, 71, 71, 71, 71, 71, 71, 1, 1, 8, 8, 1, 11, 11, 71, 71, 71] 106 rigid atoms, others: [3, 4, 5, 6, 7, 21, 22, 25] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237776 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237776 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237776/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237776 Building REAL300000237777 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237777' /scratch/stefan/7769818/working/building/REAL300000237777 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237777 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237777/0 /scratch/stefan/7769818/working/building/REAL300000237777 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/777 `/scratch/stefan/7769818/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1) `REAL300000237777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237777 none O=C([O-])C1=CC=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 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, 94, 94, 63, 63, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 94, 94, 94, 94, 63, 63, 1, 1, 1, 94] 94 rigid atoms, others: [10, 12, 13, 14, 15, 16, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 209 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237777 none O=C([O-])C1=CC=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 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, 5, 5, 33, 33, 94, 94, 59, 94, 94, 94, 94, 94, 94, 1, 1, 1, 1, 5, 5, 94, 94, 94, 1] 94 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30]) total number of confs: 285 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237777 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237777 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237777/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237777 Building REAL300000237778 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237778' /scratch/stefan/7769818/working/building/REAL300000237778 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237778 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237778/0 /scratch/stefan/7769818/working/building/REAL300000237778 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/778 `/scratch/stefan/7769818/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1) `REAL300000237778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237778 none O=C([O-])C1=CSC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 120, 120, 120, 63, 63, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 120, 120, 63, 63, 1, 1, 1, 120] 120 rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 19, 20, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 28]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237778 none O=C([O-])C1=CSC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 70, 71, 120, 120, 105, 120, 120, 120, 120, 120, 120, 1, 1, 12, 12, 120, 120, 120, 1] 120 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237778 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237778 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237778/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237778 Building REAL300000237779 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237779' /scratch/stefan/7769818/working/building/REAL300000237779 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237779 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237779/0 /scratch/stefan/7769818/working/building/REAL300000237779 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/779 `/scratch/stefan/7769818/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1OCCC(=O)[O-]) `REAL300000237779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237779 none COC1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 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, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 39, 39, 39, 13, 13, 7, 1, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 39, 39, 39, 39, 134, 183, 183, 201, 188, 74, 74, 74, 39, 13, 13, 1, 1, 1, 39, 39, 183, 183, 183, 183] 201 rigid atoms, others: [34, 35, 36, 7, 9, 10, 11, 12, 13, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 598 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237779 none COC1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 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, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 39, 39, 17, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 9, 16, 16, 29, 27, 3, 3, 3, 1, 5, 5, 39, 39, 39, 1, 1, 16, 16, 16, 16] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 19, 20, 21, 22, 37, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 222 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237779 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237779 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237779/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237779 Building REAL300000237780 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237780' /scratch/stefan/7769818/working/building/REAL300000237780 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237780 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237780/0 /scratch/stefan/7769818/working/building/REAL300000237780 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/780 `/scratch/stefan/7769818/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C(Cl)=C1) `REAL300000237780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237780 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 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 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, 93, 105, 105, 71, 71, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 105, 105, 105, 105, 105, 71, 71, 1, 1, 1, 105] 105 rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 287 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237780 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 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 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, 1, 1, 1, 10, 10, 66, 66, 105, 105, 87, 105, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 10, 10, 105, 105, 105, 1] 105 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30]) total number of confs: 292 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237780 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237780 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237780/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237780 Building REAL300000237781 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237781' /scratch/stefan/7769818/working/building/REAL300000237781 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237781 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237781/0 /scratch/stefan/7769818/working/building/REAL300000237781 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/781 `/scratch/stefan/7769818/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1) `REAL300000237781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237781 none O=C([O-])C1=C(Cl)C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 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, 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 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, 174, 174, 174, 81, 81, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 174, 174, 174, 81, 81, 1, 1, 1, 174, 174, 174] 174 rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 19, 20, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 328 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237781 none O=C([O-])C1=C(Cl)C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 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, 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 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 9, 9, 62, 62, 174, 174, 116, 174, 174, 174, 174, 174, 173, 1, 1, 1, 9, 9, 174, 174, 174, 1, 1, 1] 174 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 29, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28]) total number of confs: 520 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237781 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237781 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237781/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237781 Building REAL300000237782 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237782' /scratch/stefan/7769818/working/building/REAL300000237782 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237782 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237782/0 /scratch/stefan/7769818/working/building/REAL300000237782 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/782 `/scratch/stefan/7769818/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1O) `REAL300000237782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237782 none O=C([O-])C1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 320 conformations in input total number of sets (complete confs): 320 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 160, 160, 78, 78, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 160, 160, 160, 160, 160, 78, 78, 1, 1, 1, 159, 160, 320] 320 rigid atoms, others: [8, 10, 11, 12, 13, 14, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 32, 15, 16, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 636 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237782 none O=C([O-])C1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 320 conformations in input total number of sets (complete confs): 320 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 5, 5, 43, 43, 160, 160, 114, 160, 160, 160, 160, 160, 160, 1, 1, 1, 1, 1, 5, 5, 160, 160, 160, 1, 1, 2] 320 rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 30, 31] set([0, 32, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29]) total number of confs: 442 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237782 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237782 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237782/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237782 Building REAL300000237783 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237783' /scratch/stefan/7769818/working/building/REAL300000237783 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237783 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237783/0 /scratch/stefan/7769818/working/building/REAL300000237783 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/783 `/scratch/stefan/7769818/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F) `REAL300000237783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237783 none CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 73, 73, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 117, 117, 117, 117, 117, 117, 117, 117, 73, 73, 1, 1, 1] 117 rigid atoms, others: [35, 36, 37, 13, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 254 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237783 none CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 2, 2, 1, 1, 1, 9, 9, 64, 64, 117, 117, 95, 117, 117, 117, 117, 117, 117, 2, 2, 2, 1, 2, 2, 2, 1, 9, 9, 117, 117, 117] 117 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 9, 10, 11, 28] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 326 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237783 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237783 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237783/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237783 Building REAL300000237784 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237784' /scratch/stefan/7769818/working/building/REAL300000237784 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237784 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237784/0 /scratch/stefan/7769818/working/building/REAL300000237784 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/784 `/scratch/stefan/7769818/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1)C(=O)[O-]) `REAL300000237784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237784 none CC(OC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 11, 11, 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, 7, 7, 7, 7, 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, 182, 39, 39, 105, 105, 39, 39, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 105, 105, 201, 201, 201, 201, 201, 201, 201, 105, 105, 39, 39, 1, 1, 1, 105, 105] 201 rigid atoms, others: [34, 35, 36, 9, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 614 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237784 none CC(OC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 11, 11, 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, 7, 7, 7, 7, 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: [14, 6, 1, 1, 1, 1, 1, 1, 5, 5, 35, 35, 105, 105, 45, 105, 105, 105, 105, 105, 105, 1, 1, 14, 19, 19, 14, 14, 14, 14, 1, 1, 5, 5, 105, 105, 105, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 21, 22, 38, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 401 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237784 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237784 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237784/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237784 Building REAL300000237785 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237785' /scratch/stefan/7769818/working/building/REAL300000237785 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237785 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237785/0 /scratch/stefan/7769818/working/building/REAL300000237785 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/785 `/scratch/stefan/7769818/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F) `REAL300000237785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237785 none O=C([O-])CCOC1=CC=CC=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 169, 126, 61, 61, 61, 42, 61, 61, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 169, 169, 61, 61, 61, 61, 26, 26, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 14, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 685 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237785 none O=C([O-])CCOC1=CC=CC=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 51, 66, 33, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 61, 61, 33, 61, 61, 61, 61, 61, 61, 51, 51, 33, 33, 1, 1, 1, 1, 7, 7, 61, 61, 61] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 460 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237785 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237785 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237785/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237785 Building REAL300000237786 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237786' /scratch/stefan/7769818/working/building/REAL300000237786 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237786 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237786/0 /scratch/stefan/7769818/working/building/REAL300000237786 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/786 `/scratch/stefan/7769818/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)[O-])=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F) `REAL300000237786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237786 none CN1N=CC(C(=O)[O-])=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 98, 98, 98, 98, 98, 59, 59, 13, 1, 13, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 98, 98, 98, 98, 59, 59, 1, 1, 1] 98 rigid atoms, others: [11, 13, 14, 15, 16, 17, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 23, 24, 25, 26, 27, 28]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237786 none CN1N=CC(C(=O)[O-])=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 9, 9, 46, 46, 98, 98, 79, 98, 98, 98, 98, 98, 98, 2, 2, 2, 1, 9, 9, 98, 98, 98] 98 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 26] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237786 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237786 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237786/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237786 Building REAL300000237787 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237787' /scratch/stefan/7769818/working/building/REAL300000237787 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237787 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237787/0 /scratch/stefan/7769818/working/building/REAL300000237787 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/787 `/scratch/stefan/7769818/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1F) `REAL300000237787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237787 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 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 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 139, 139, 139, 69, 69, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 139, 139, 139, 139, 139, 69, 69, 1, 1, 1, 139] 139 rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 286 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237787 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 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 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 38, 38, 139, 139, 66, 139, 139, 139, 139, 139, 139, 1, 1, 1, 1, 1, 5, 5, 139, 139, 139, 1] 139 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30]) total number of confs: 490 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237787 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237787 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237787/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237787 Building REAL300000237788 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237788' /scratch/stefan/7769818/working/building/REAL300000237788 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237788 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237788/0 /scratch/stefan/7769818/working/building/REAL300000237788 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/788 `/scratch/stefan/7769818/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)O1) `REAL300000237788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237788 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 12, 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, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 142, 142, 142, 142, 65, 65, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 142, 201, 201, 142, 142, 65, 65, 1, 1, 1] 201 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 472 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237788 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 12, 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, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 12, 28, 12, 1, 1, 1, 1, 1, 1, 11, 11, 53, 53, 142, 142, 83, 142, 142, 142, 142, 142, 142, 1, 13, 12, 1, 1, 11, 11, 142, 142, 142] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 491 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237788 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237788 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237788/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237788 Building REAL300000237789 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237789' /scratch/stefan/7769818/working/building/REAL300000237789 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237789 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237789/0 /scratch/stefan/7769818/working/building/REAL300000237789 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/789 `/scratch/stefan/7769818/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1C(=O)[O-]) `REAL300000237789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237789 none COC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1C(=O)[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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 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, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 143, 143, 143, 143, 63, 63, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 143, 143, 143, 201, 201, 201, 201, 201, 143, 143, 63, 63, 1, 1, 1, 143] 201 rigid atoms, others: [32, 33, 34, 8, 10, 11, 12, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 625 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237789 none COC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1C(=O)[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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 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, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 143, 143, 80, 143, 143, 143, 143, 143, 143, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 5, 5, 143, 143, 143, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 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]) total number of confs: 462 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237789 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237789 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237789/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237789 Building REAL300000237790 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237790' /scratch/stefan/7769818/working/building/REAL300000237790 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237790 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237790/0 /scratch/stefan/7769818/working/building/REAL300000237790 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/790 `/scratch/stefan/7769818/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1) `REAL300000237790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237790 none O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 3, 3, 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, 142, 142, 142, 72, 72, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 142, 142, 142, 72, 72, 1, 1, 1, 142] 142 rigid atoms, others: [11, 13, 14, 15, 16, 17, 20, 21, 22, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 23, 24, 25, 26, 27, 31]) total number of confs: 282 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237790 none O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 11, 11, 73, 73, 142, 142, 113, 142, 142, 142, 142, 142, 140, 1, 1, 1, 11, 11, 142, 142, 142, 1] 142 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 390 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237790 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237790 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237790/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237790 Building REAL300000237791 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237791' /scratch/stefan/7769818/working/building/REAL300000237791 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237791 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237791/0 /scratch/stefan/7769818/working/building/REAL300000237791 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/791 `/scratch/stefan/7769818/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F) `REAL300000237791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237791 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 101, 101, 101, 101, 101, 148, 101, 101, 143, 143, 101, 31, 31, 11, 1, 11, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 142, 142, 142, 101, 148, 148, 148, 101, 31, 31, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 15, 17, 18, 19, 20, 21, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 521 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237791 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 3, 3, 1, 1, 1, 9, 9, 27, 27, 101, 101, 61, 101, 101, 101, 101, 101, 101, 4, 4, 4, 1, 3, 3, 3, 1, 9, 9, 101, 101, 101] 201 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 11, 12, 34, 13, 30] set([0, 6, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 347 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237791 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237791 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237791/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237791 Building REAL300000237792 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237792' /scratch/stefan/7769818/working/building/REAL300000237792 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237792 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237792/0 /scratch/stefan/7769818/working/building/REAL300000237792 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/792 `/scratch/stefan/7769818/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1F) `REAL300000237792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237792 none O=C([O-])C1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 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 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 186, 186, 186, 88, 88, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 186, 186, 186, 186, 186, 88, 88, 1, 1, 1, 186, 186] 186 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 352 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237792 none O=C([O-])C1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 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 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 6, 42, 42, 186, 186, 83, 186, 186, 186, 186, 186, 183, 1, 1, 1, 1, 1, 6, 6, 186, 186, 186, 1, 1] 186 rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29]) total number of confs: 596 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237792 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237792 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237792/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237792 Building REAL300000237793 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237793' /scratch/stefan/7769818/working/building/REAL300000237793 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237793 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237793/0 /scratch/stefan/7769818/working/building/REAL300000237793 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/793 `/scratch/stefan/7769818/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1) `REAL300000237793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237793 none O=C([O-])CC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 88, 88, 98, 98, 64, 64, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 98, 98, 98, 98, 98, 98, 64, 64, 1, 1, 1, 98, 98] 98 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 305 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237793 none O=C([O-])CC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 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, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 41, 41, 98, 98, 97, 98, 98, 98, 98, 98, 98, 1, 1, 2, 2, 1, 1, 6, 6, 98, 98, 98, 1, 1] 98 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: 194 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237793 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237793 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237793/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237793 Building REAL300000237794 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237794' /scratch/stefan/7769818/working/building/REAL300000237794 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237794 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237794/0 /scratch/stefan/7769818/working/building/REAL300000237794 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/794 `/scratch/stefan/7769818/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(Br)=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1) `REAL300000237794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237794 none O=C([O-])C1=CC(Br)=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 3, 3, 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, 109, 109, 109, 109, 109, 73, 73, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 73, 73, 1, 1, 1, 109] 109 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 31]) total number of confs: 231 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237794 none O=C([O-])C1=CC(Br)=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 3, 3, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 41, 41, 109, 109, 109, 109, 109, 109, 109, 109, 109, 1, 1, 1, 5, 5, 109, 109, 109, 1] 109 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237794 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237794 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237794/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237794 Building REAL300000237795 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237795' /scratch/stefan/7769818/working/building/REAL300000237795 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237795 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237795/0 /scratch/stefan/7769818/working/building/REAL300000237795 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/795 `/scratch/stefan/7769818/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)S1) `REAL300000237795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237795 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 96, 96, 47, 47, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 96, 96, 96, 47, 47, 1, 1, 1] 96 rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 19, 20, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 25]) total number of confs: 191 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237795 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 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, 2, 1, 1, 1, 1, 1, 11, 11, 59, 59, 96, 96, 71, 95, 96, 96, 96, 96, 96, 1, 1, 1, 11, 11, 96, 96, 96] 96 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28]) total number of confs: 299 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237795 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237795 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237795/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237795 Building REAL300000237796 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237796' /scratch/stefan/7769818/working/building/REAL300000237796 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237796 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237796/0 /scratch/stefan/7769818/working/building/REAL300000237796 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/796 `/scratch/stefan/7769818/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1) `REAL300000237796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237796 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 123, 81, 149, 149, 81, 81, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 149, 149, 149, 149, 149, 149, 81, 81, 1, 1, 1, 149, 149] 149 rigid atoms, others: [32, 33, 11, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 644 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237796 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 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, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [10, 3, 10, 3, 1, 1, 1, 1, 1, 1, 5, 5, 46, 46, 149, 149, 91, 149, 149, 149, 149, 149, 149, 1, 1, 3, 3, 1, 1, 5, 5, 149, 149, 149, 1, 1] 149 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 23, 24, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 495 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237796 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237796 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237796/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237796 Building REAL300000237797 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237797' /scratch/stefan/7769818/working/building/REAL300000237797 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237797 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237797/0 /scratch/stefan/7769818/working/building/REAL300000237797 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/797 `/scratch/stefan/7769818/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1F) `REAL300000237797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237797 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 89, 89, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 201, 201, 89, 89, 1, 1, 1, 201] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 368 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237797 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 81, 81, 201, 201, 86, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 11, 11, 201, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30]) total number of confs: 772 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237797 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237797 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237797/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237797 Building REAL300000237798 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237798' /scratch/stefan/7769818/working/building/REAL300000237798 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237798 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237798/0 /scratch/stefan/7769818/working/building/REAL300000237798 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/798 `/scratch/stefan/7769818/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NNC2=CC=CC(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)=C21) `REAL300000237798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237798 none O=C([O-])C1=NNC2=CC=CC(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 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, 71, 71, 71, 71, 71, 54, 54, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 71, 71, 71, 71, 71, 54, 54, 1, 1, 1] 71 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237798 none O=C([O-])C1=NNC2=CC=CC(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 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, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 37, 37, 71, 71, 61, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 9, 9, 71, 71, 71] 71 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28, 29] set([0, 32, 2, 34, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237798 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237798 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237798/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237798 Building REAL300000237799 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237799' /scratch/stefan/7769818/working/building/REAL300000237799 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237799 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237799/0 /scratch/stefan/7769818/working/building/REAL300000237799 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/799 `/scratch/stefan/7769818/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C(C2=CC=CC=C2)=N1) `REAL300000237799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237799 none O=C([O-])CN1C=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 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, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 128, 128, 128, 48, 48, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 128, 128, 163, 163, 163, 163, 163, 128, 201, 201, 128, 48, 48, 1, 1, 1, 163, 163, 163, 163, 163] 201 rigid atoms, others: [34, 35, 36, 9, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 683 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237799 none O=C([O-])CN1C=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 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, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 20, 5, 5, 5, 5, 5, 21, 21, 61, 61, 163, 163, 94, 163, 163, 163, 163, 163, 163, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 21, 21, 163, 163, 163, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 560 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: REAL300000237799 none O=C([O-])CN1C=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 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, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 11, 1, 1, 1, 1, 1, 11, 11, 40, 40, 128, 128, 72, 127, 128, 128, 128, 128, 128, 1, 1, 5, 5, 1, 5, 5, 1, 6, 6, 1, 11, 11, 128, 128, 128, 5, 5, 4, 5, 5] 201 rigid atoms, others: [3, 4, 5, 6, 7, 21, 22, 28, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 430 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237799 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237799 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237799/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237799 Building REAL300000237800 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237800' /scratch/stefan/7769818/working/building/REAL300000237800 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237800 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237800/0 /scratch/stefan/7769818/working/building/REAL300000237800 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/800 `/scratch/stefan/7769818/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)O2)C=C1O) `REAL300000237800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237800 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)O2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'O.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 4, 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: [21, 12, 21, 12, 13, 13, 1, 1, 1, 1, 1, 1, 11, 11, 32, 32, 79, 79, 44, 79, 79, 79, 79, 79, 79, 1, 13, 13, 13, 13, 13, 1, 1, 11, 11, 79, 79, 79, 13, 26] 402 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 25, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237800 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)O2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'O.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 79, 79, 79, 79, 40, 40, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 79, 201, 201, 201, 201, 201, 79, 79, 40, 40, 1, 1, 1, 201, 402] 402 rigid atoms, others: [35, 36, 37, 13, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 749 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: REAL300000237800 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)O2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'O.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 4, 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: [3, 1, 3, 1, 1, 1, 1, 1, 13, 13, 13, 13, 55, 55, 136, 136, 201, 201, 172, 201, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 1, 13, 13, 54, 55, 201, 201, 201, 1, 2] 402 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 26, 27, 28, 29, 30] set([0, 2, 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, 39]) total number of confs: 594 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237800 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237800 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237800/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237800 Building REAL300000237801 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237801' /scratch/stefan/7769818/working/building/REAL300000237801 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237801 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237801/0 /scratch/stefan/7769818/working/building/REAL300000237801 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/801 `/scratch/stefan/7769818/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)C=C2)C=C1) `REAL300000237801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237801 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 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, 7, 7, 7, 7, 3, 7, 7, 7, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 51, 51, 39, 51, 51, 51, 51, 51, 51, 1, 1, 3, 3, 3, 3, 1, 1, 3, 3, 51, 51, 51, 1, 1, 3, 3] 71 rigid atoms, others: [32, 38, 6, 7, 8, 9, 10, 11, 25, 26, 39, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237801 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 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, 7, 7, 7, 7, 3, 7, 7, 7, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 51, 71, 51, 71, 71, 51, 51, 51, 51, 51, 51, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 51, 51, 71, 71, 71, 71, 51, 51, 51, 51, 1, 1, 1, 51, 51, 71, 71] 71 rigid atoms, others: [35, 36, 37, 13, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 311 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: REAL300000237801 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 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, 7, 7, 7, 7, 3, 7, 7, 7, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 5, 5, 31, 31, 71, 71, 64, 71, 71, 71, 71, 71, 71, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 71, 71, 71, 3, 3, 1, 1] 71 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237801 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237801 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237801/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237801 Building REAL300000237802 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237802' /scratch/stefan/7769818/working/building/REAL300000237802 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237802 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237802/0 /scratch/stefan/7769818/working/building/REAL300000237802 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/802 `/scratch/stefan/7769818/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2NC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)C2=C1) `REAL300000237802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237802 none O=C([O-])C1=CC=C2NC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 151, 151, 151, 151, 151, 151, 61, 61, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 151, 151, 151, 151, 151, 151, 61, 61, 1, 1, 1, 151] 151 rigid atoms, others: [32, 33, 34, 12, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237802 none O=C([O-])C1=CC=C2NC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 74, 75, 151, 151, 104, 151, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 1, 11, 12, 151, 151, 151, 1] 151 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 35, 24, 25, 26, 27, 28, 29] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31]) total number of confs: 470 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237802 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237802 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237802/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237802 Building REAL300000237803 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237803' /scratch/stefan/7769818/working/building/REAL300000237803 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237803 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237803/0 /scratch/stefan/7769818/working/building/REAL300000237803 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/803 `/scratch/stefan/7769818/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=N1) `REAL300000237803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237803 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 72, 50, 50, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 72, 72, 72, 72, 50, 50, 1, 1, 1, 72] 72 rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 173 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237803 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 39, 39, 72, 72, 58, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 5, 5, 72, 72, 72, 1] 72 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 213 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237803 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237803 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237803/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237803 Building REAL300000237804 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237804' /scratch/stefan/7769818/working/building/REAL300000237804 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237804 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237804/0 /scratch/stefan/7769818/working/building/REAL300000237804 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/804 `/scratch/stefan/7769818/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1O) `REAL300000237804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237804 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 256 conformations in input total number of sets (complete confs): 256 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 128, 128, 128, 71, 71, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 128, 128, 128, 128, 128, 71, 71, 1, 1, 1, 128, 256] 256 rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 32, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 526 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237804 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 256 conformations in input total number of sets (complete confs): 256 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 44, 44, 128, 128, 49, 128, 128, 128, 128, 128, 128, 1, 1, 1, 1, 1, 6, 6, 128, 128, 128, 1, 2] 256 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 31] set([0, 32, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30]) total number of confs: 472 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237804 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237804 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237804/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237804 Building REAL300000237805 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237805' /scratch/stefan/7769818/working/building/REAL300000237805 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237805 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237805/0 /scratch/stefan/7769818/working/building/REAL300000237805 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/805 `/scratch/stefan/7769818/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1C(=O)[O-]) `REAL300000237805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237805 none CC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 187, 187, 91, 91, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 187, 187, 187, 187, 187, 187, 187, 187, 187, 187, 91, 91, 1, 1, 1, 187] 187 rigid atoms, others: [32, 33, 7, 9, 10, 11, 12, 13, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 359 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237805 none CC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 43, 43, 187, 187, 69, 187, 187, 187, 187, 187, 187, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 6, 6, 187, 187, 187, 1] 187 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 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]) total number of confs: 621 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237805 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237805 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237805/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237805 Building REAL300000237806 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237806' /scratch/stefan/7769818/working/building/REAL300000237806 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237806 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237806/0 /scratch/stefan/7769818/working/building/REAL300000237806 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/806 `/scratch/stefan/7769818/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)SC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1) `REAL300000237806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237806 none O=C([O-])C1=C(Cl)SC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 67, 67, 13, 1, 13, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 67, 67, 1, 1, 1, 201] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 22, 23, 24, 28]) total number of confs: 342 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237806 none O=C([O-])C1=C(Cl)SC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 98, 98, 201, 201, 156, 201, 201, 201, 201, 201, 201, 1, 13, 13, 201, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 22, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 559 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237806 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237806 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237806/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237806 Building REAL300000237807 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237807' /scratch/stefan/7769818/working/building/REAL300000237807 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237807 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237807/0 /scratch/stefan/7769818/working/building/REAL300000237807 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/807 `/scratch/stefan/7769818/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)O1) `REAL300000237807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237807 none CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 12, 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, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 189, 189, 189, 189, 189, 83, 83, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 189, 189, 189, 189, 189, 83, 83, 1, 1, 1] 189 rigid atoms, others: [10, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 345 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237807 none CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 12, 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, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 12, 12, 85, 85, 189, 189, 85, 189, 189, 189, 189, 189, 189, 1, 2, 2, 2, 1, 12, 12, 189, 189, 189] 189 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 22, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 727 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237807 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237807 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237807/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237807 Building REAL300000237808 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237808' /scratch/stefan/7769818/working/building/REAL300000237808 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237808 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237808/0 /scratch/stefan/7769818/working/building/REAL300000237808 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/808 `/scratch/stefan/7769818/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)S2)C=C1) `REAL300000237808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237808 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 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, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 11, 11, 80, 80, 150, 150, 105, 150, 150, 150, 150, 150, 150, 1, 7, 7, 7, 7, 1, 1, 11, 11, 150, 150, 150, 7, 7] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 477 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237808 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 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, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 150, 201, 150, 201, 201, 150, 150, 150, 150, 49, 49, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 150, 201, 201, 201, 201, 150, 150, 49, 49, 1, 1, 1, 201, 201] 201 rigid atoms, others: [34, 35, 36, 13, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 668 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: REAL300000237808 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 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, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 8, 8, 57, 57, 150, 150, 201, 201, 185, 201, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 8, 8, 57, 57, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 26, 27, 28, 29, 37] set([0, 2, 8, 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: 553 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237808 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237808 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237808/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237808 Building REAL300000237809 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237809' /scratch/stefan/7769818/working/building/REAL300000237809 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237809 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237809/0 /scratch/stefan/7769818/working/building/REAL300000237809 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/809 `/scratch/stefan/7769818/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F) `REAL300000237809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237809 none CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 104, 104, 104, 104, 104, 61, 61, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 61, 61, 1, 1, 1] 104 rigid atoms, others: [11, 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, 12, 23, 24, 25, 26, 27, 28]) total number of confs: 216 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237809 none CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 60, 60, 104, 104, 90, 104, 104, 104, 104, 104, 104, 2, 2, 2, 1, 10, 10, 104, 104, 104] 104 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 26] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237809 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237809 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237809/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237809 Building REAL300000237810 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237810' /scratch/stefan/7769818/working/building/REAL300000237810 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237810 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237810/0 /scratch/stefan/7769818/working/building/REAL300000237810 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/810 `/scratch/stefan/7769818/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)O2)=CC=C1O) `REAL300000237810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237810 none O=C([O-])C1=CC(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 4, 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: [23, 12, 23, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 37, 37, 96, 96, 37, 96, 96, 96, 96, 96, 96, 1, 12, 12, 12, 12, 12, 1, 1, 12, 12, 96, 96, 96, 12, 12, 24] 402 rigid atoms, others: [5, 6, 7, 8, 9, 10, 24, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 416 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237810 none O=C([O-])C1=CC(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 96, 96, 96, 96, 45, 45, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 96, 201, 201, 201, 201, 201, 96, 96, 45, 45, 1, 1, 1, 201, 201, 402] 402 rigid atoms, others: [34, 35, 36, 12, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 737 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237810 none O=C([O-])C1=CC(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 4, 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: [3, 1, 3, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 103, 103, 201, 201, 103, 201, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 1, 12, 12, 50, 50, 201, 201, 201, 1, 1, 2] 402 rigid atoms, others: [1, 3, 4, 5, 6, 38, 25, 26, 27, 28, 29, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 751 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237810 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237810 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237810/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237810 Building REAL300000237811 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237811' /scratch/stefan/7769818/working/building/REAL300000237811 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237811 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237811/0 /scratch/stefan/7769818/working/building/REAL300000237811 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/811 `/scratch/stefan/7769818/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1) `REAL300000237811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237811 none O=C([O-])C1=CN=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 94, 94, 94, 63, 63, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 94, 94, 94, 63, 63, 1, 1, 1, 94] 94 rigid atoms, others: [10, 12, 13, 14, 15, 16, 19, 20, 21, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 22, 23, 24, 25, 26, 30]) total number of confs: 209 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237811 none O=C([O-])C1=CN=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 33, 33, 94, 94, 94, 94, 94, 94, 94, 94, 94, 1, 1, 1, 5, 5, 94, 94, 94, 1] 94 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237811 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237811 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237811/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237811 Building REAL300000237812 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237812' /scratch/stefan/7769818/working/building/REAL300000237812 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237812 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237812/0 /scratch/stefan/7769818/working/building/REAL300000237812 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/812 `/scratch/stefan/7769818/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=COC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1) `REAL300000237812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237812 none O=C([O-])C1=COC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 99, 99, 58, 58, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 99, 99, 58, 58, 1, 1, 1, 99] 99 rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 19, 20, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 28]) total number of confs: 211 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237812 none O=C([O-])C1=COC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 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, 13, 13, 60, 60, 99, 99, 99, 99, 99, 99, 99, 99, 99, 1, 1, 13, 13, 99, 99, 99, 1] 99 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237812 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237812 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237812/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237812 Building REAL300000237813 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237813' /scratch/stefan/7769818/working/building/REAL300000237813 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237813 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237813/0 /scratch/stefan/7769818/working/building/REAL300000237813 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/813 `/scratch/stefan/7769818/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)S2)=C1) `REAL300000237813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237813 none O=C([O-])C1=CC=CC(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 14, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 11, 11, 40, 40, 104, 104, 42, 104, 104, 104, 104, 104, 104, 1, 12, 12, 12, 12, 1, 1, 11, 11, 104, 104, 104, 12] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 26, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 389 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237813 none O=C([O-])C1=CC=CC(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 14, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 104, 104, 104, 104, 27, 27, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 104, 201, 201, 201, 201, 104, 104, 27, 27, 1, 1, 1, 201] 201 rigid atoms, others: [35, 36, 37, 14, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 319 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: REAL300000237813 none O=C([O-])C1=CC=CC(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 14, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 12, 12, 82, 82, 149, 149, 201, 201, 155, 201, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 12, 12, 82, 82, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 665 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237813 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237813 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237813/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237813 Building REAL300000237814 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237814' /scratch/stefan/7769818/working/building/REAL300000237814 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237814 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237814/0 /scratch/stefan/7769818/working/building/REAL300000237814 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/814 `/scratch/stefan/7769818/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F) `REAL300000237814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237814 none COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F 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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 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, 2, 2, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 77, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 201, 201, 201, 201, 77, 77, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 13, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 354 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237814 none COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F 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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 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, 2, 2, 7, 7, 7, 7, 7, 3, 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 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, 1, 1, 1, 9, 9, 75, 75, 201, 201, 126, 201, 201, 201, 201, 201, 201, 4, 4, 4, 1, 1, 1, 9, 9, 201, 201, 201] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 28, 29, 30] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 609 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237814 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237814 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237814/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237814 Building REAL300000237815 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237815' /scratch/stefan/7769818/working/building/REAL300000237815 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237815 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237815/0 /scratch/stefan/7769818/working/building/REAL300000237815 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/815 `/scratch/stefan/7769818/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2SC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)C2=C1) `REAL300000237815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237815 none O=C([O-])C1=CC=C2SC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 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, 7, 7, 7, 3, 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 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 126, 126, 126, 126, 126, 126, 59, 59, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 126, 126, 126, 126, 126, 59, 59, 1, 1, 1, 126] 126 rigid atoms, others: [32, 33, 12, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 238 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237815 none O=C([O-])C1=CC=C2SC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 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, 7, 7, 7, 3, 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 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 66, 66, 126, 126, 126, 126, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 11, 11, 126, 126, 126, 1] 126 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28] set([0, 32, 2, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31]) total number of confs: 249 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237815 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237815 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237815/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237815 Building REAL300000237816 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237816' /scratch/stefan/7769818/working/building/REAL300000237816 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237816 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237816/0 /scratch/stefan/7769818/working/building/REAL300000237816 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/816 `/scratch/stefan/7769818/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Br)C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1) `REAL300000237816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237816 none O=C([O-])C1=CC=C(Br)C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 116, 116, 116, 116, 75, 75, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 116, 116, 116, 75, 75, 1, 1, 1, 116] 116 rigid atoms, others: [11, 13, 14, 15, 16, 17, 20, 21, 22, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 23, 24, 25, 26, 27, 31]) total number of confs: 256 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237816 none O=C([O-])C1=CC=C(Br)C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 3, 3, 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, 9, 9, 67, 67, 116, 116, 102, 116, 116, 116, 116, 116, 116, 1, 1, 1, 9, 9, 116, 116, 116, 1] 116 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 290 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237816 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237816 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237816/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237816 Building REAL300000237817 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237817' /scratch/stefan/7769818/working/building/REAL300000237817 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237817 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237817/0 /scratch/stefan/7769818/working/building/REAL300000237817 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/817 `/scratch/stefan/7769818/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C([N+](=O)[O-])=C1) `REAL300000237817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237817 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 92, 92, 92, 72, 72, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 92, 92, 92, 92, 92, 92, 92, 72, 72, 1, 1, 1, 92] 92 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 213 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237817 none O=C([O-])C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 40, 40, 92, 92, 53, 92, 92, 92, 92, 92, 92, 1, 1, 2, 2, 1, 1, 1, 6, 6, 92, 92, 92, 1] 92 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 33, 21, 22, 25, 26, 27] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 28, 29, 30, 31]) total number of confs: 296 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237817 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237817 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237817/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237817 Building REAL300000237818 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237818' /scratch/stefan/7769818/working/building/REAL300000237818 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237818 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237818/0 /scratch/stefan/7769818/working/building/REAL300000237818 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/818 `/scratch/stefan/7769818/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1) `REAL300000237818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237818 none O=C([O-])CC1=CC=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 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, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 153, 153, 140, 153, 153, 87, 87, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 153, 201, 201, 151, 153, 153, 87, 87, 1, 1, 1, 153] 201 rigid atoms, others: [32, 33, 11, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 661 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237818 none O=C([O-])CC1=CC=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 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, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 45, 45, 153, 153, 108, 153, 153, 153, 153, 153, 153, 1, 2, 2, 1, 1, 1, 5, 5, 153, 153, 153, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 23, 26, 27, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 435 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237818 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237818 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237818/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237818 Building REAL300000237819 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237819' /scratch/stefan/7769818/working/building/REAL300000237819 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237819 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237819/0 /scratch/stefan/7769818/working/building/REAL300000237819 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/819 `/scratch/stefan/7769818/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1C(=O)[O-]) `REAL300000237819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237819 none COC1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 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, 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] 0 hydrogens 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, 146, 146, 146, 60, 60, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 146, 146, 146, 146, 201, 201, 201, 201, 201, 146, 60, 60, 1, 1, 1, 146, 146] 201 rigid atoms, others: [32, 33, 7, 9, 10, 11, 12, 13, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 615 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237819 none COC1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 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, 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] 0 hydrogens 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, 6, 6, 40, 40, 146, 146, 50, 146, 146, 146, 146, 146, 146, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 6, 6, 146, 146, 146, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 19, 20, 21, 22, 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]) total number of confs: 486 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237819 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237819 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237819/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237819 Building REAL300000237820 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237820' /scratch/stefan/7769818/working/building/REAL300000237820 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237820 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237820/0 /scratch/stefan/7769818/working/building/REAL300000237820 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/820 `/scratch/stefan/7769818/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C(F)=C1) `REAL300000237820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237820 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 61, 65, 65, 65, 50, 50, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 65, 65, 65, 65, 50, 50, 1, 1, 1, 65] 65 rigid atoms, others: [10, 12, 13, 14, 15, 16, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237820 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 34, 34, 66, 66, 66, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 6, 6, 66, 66, 66, 1] 66 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237820 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237820 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237820/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237820 Building REAL300000237821 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237821' /scratch/stefan/7769818/working/building/REAL300000237821 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237821 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237821/0 /scratch/stefan/7769818/working/building/REAL300000237821 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/821 `/scratch/stefan/7769818/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C(F)C=C1) `REAL300000237821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237821 none O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 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 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, 71, 71, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 201, 201, 71, 71, 1, 1, 1, 201, 201] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 341 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237821 none O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 11, 11, 77, 77, 201, 201, 125, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 11, 11, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 615 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237821 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237821 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237821/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237821 Building REAL300000237822 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237822' /scratch/stefan/7769818/working/building/REAL300000237822 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237822 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237822/0 /scratch/stefan/7769818/working/building/REAL300000237822 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/822 `/scratch/stefan/7769818/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CS1) `REAL300000237822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237822 none O=C([O-])C1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 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, 62, 62, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 87, 87, 87, 62, 62, 1, 1, 1, 87] 87 rigid atoms, others: [8, 10, 11, 12, 13, 14, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 20, 21, 22, 23, 24, 28]) total number of confs: 197 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237822 none O=C([O-])C1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 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, 7, 7, 42, 42, 87, 87, 52, 87, 87, 87, 87, 87, 87, 1, 1, 1, 7, 7, 87, 87, 87, 1] 87 rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237822 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237822 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237822/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237822 Building REAL300000237823 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237823' /scratch/stefan/7769818/working/building/REAL300000237823 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237823 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237823/0 /scratch/stefan/7769818/working/building/REAL300000237823 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/823 `/scratch/stefan/7769818/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1OCC(=O)[O-]) `REAL300000237823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237823 none CCOC1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 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: [76, 59, 29, 29, 29, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 29, 29, 29, 29, 117, 198, 200, 200, 76, 76, 76, 76, 76, 29, 9, 9, 1, 1, 1, 29, 29, 198, 198] 201 rigid atoms, others: [36, 37, 38, 8, 10, 11, 12, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 768 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237823 none CCOC1=CC(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', '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, 5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 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: [9, 6, 1, 1, 1, 1, 1, 5, 5, 13, 13, 29, 29, 21, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 7, 26, 43, 43, 9, 9, 9, 9, 9, 1, 5, 5, 29, 29, 29, 1, 1, 26, 26] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 39, 40, 20, 21, 22, 23] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 269 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237823 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237823 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237823/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237823 Building REAL300000237824 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237824' /scratch/stefan/7769818/working/building/REAL300000237824 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237824 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237824/0 /scratch/stefan/7769818/working/building/REAL300000237824 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/824 `/scratch/stefan/7769818/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1F) `REAL300000237824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237824 none O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 85, 66, 85, 85, 85, 66, 66, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 85, 85, 85, 85, 66, 66, 1, 1, 1, 85] 85 rigid atoms, others: [10, 12, 13, 14, 15, 16, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 294 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237824 none O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 22, 22, 85, 85, 36, 85, 85, 85, 85, 85, 85, 1, 1, 1, 1, 3, 3, 85, 85, 85, 1] 85 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30]) total number of confs: 270 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237824 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237824 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237824/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237824 Building REAL300000237825 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237825' /scratch/stefan/7769818/working/building/REAL300000237825 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237825 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237825/0 /scratch/stefan/7769818/working/building/REAL300000237825 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/825 `/scratch/stefan/7769818/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)O2)N1) `REAL300000237825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237825 none O=C([O-])C1=CC2=C(C=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)O2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 4, 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: [78, 78, 78, 78, 78, 78, 78, 78, 46, 46, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 78, 78, 78, 78, 46, 46, 1, 1, 1, 78] 79 rigid atoms, others: [11, 13, 14, 15, 16, 17, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 32, 23, 24, 25, 26, 27, 28]) total number of confs: 167 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237825 none O=C([O-])C1=CC2=C(C=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)O2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 47, 47, 78, 78, 65, 78, 79, 79, 78, 78, 78, 1, 1, 1, 1, 12, 12, 78, 78, 78, 1] 79 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237825 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237825 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237825/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237825 Building REAL300000237826 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237826' /scratch/stefan/7769818/working/building/REAL300000237826 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237826 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237826/0 /scratch/stefan/7769818/working/building/REAL300000237826 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/826 `/scratch/stefan/7769818/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)=CC=C2O1) `REAL300000237826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237826 none O=C([O-])C1=CC2=CC(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 83, 83, 83, 54, 54, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 83, 83, 83, 83, 83, 83, 54, 54, 1, 1, 1, 83, 83] 83 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 187 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237826 none O=C([O-])C1=CC2=CC(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 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, 2, 1, 1, 1, 1, 1, 1, 6, 6, 35, 35, 83, 83, 59, 83, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 1, 6, 6, 83, 83, 83, 1, 1] 83 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: 261 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237826 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237826 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237826/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237826 Building REAL300000237827 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237827' /scratch/stefan/7769818/working/building/REAL300000237827 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237827 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237827/0 /scratch/stefan/7769818/working/building/REAL300000237827 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/827 `/scratch/stefan/7769818/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)=CC=CN12) `REAL300000237827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237827 none O=C([O-])C1=CN=C2C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 141, 141, 141, 141, 141, 74, 73, 13, 1, 13, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 141, 141, 141, 141, 141, 74, 74, 1, 1, 1, 141, 141, 141] 141 rigid atoms, others: [10, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 282 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237827 none O=C([O-])C1=CN=C2C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 81, 81, 141, 141, 120, 141, 141, 141, 141, 141, 141, 1, 1, 1, 1, 1, 12, 12, 141, 141, 141, 1, 1, 1] 141 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 32, 22, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31]) total number of confs: 370 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237827 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237827 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237827/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237827 Building REAL300000237828 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237828' /scratch/stefan/7769818/working/building/REAL300000237828 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237828 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237828/0 /scratch/stefan/7769818/working/building/REAL300000237828 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/828 `/scratch/stefan/7769818/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F) `REAL300000237828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237828 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 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, 7, 7, 7, 7, 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 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, 119, 119, 119, 119, 119, 119, 58, 58, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 119, 119, 119, 119, 119, 119, 119, 58, 58, 1, 1, 1] 119 rigid atoms, others: [37, 38, 39, 16, 18, 19, 20, 21, 22, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237828 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 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, 7, 7, 7, 7, 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 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, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 59, 59, 119, 119, 88, 119, 119, 119, 119, 119, 119, 2, 2, 2, 1, 1, 1, 1, 9, 9, 119, 119, 119] 119 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 34, 31] set([4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237828 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237828 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237828/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237828 Building REAL300000237829 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237829' /scratch/stefan/7769818/working/building/REAL300000237829 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237829 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237829/0 /scratch/stefan/7769818/working/building/REAL300000237829 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/829 `/scratch/stefan/7769818/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN2C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)=CN=C2C=C1) `REAL300000237829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237829 none O=C([O-])C1=CN2C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 8, 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, 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 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 157, 157, 157, 64, 64, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 157, 157, 157, 157, 157, 157, 64, 64, 1, 1, 1, 157, 157, 157] 157 rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 287 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237829 none O=C([O-])C1=CN2C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 8, 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, 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 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 12, 74, 74, 157, 157, 157, 157, 157, 157, 157, 157, 157, 1, 1, 1, 1, 1, 1, 12, 12, 157, 157, 157, 1, 1, 1] 157 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 33, 21, 22, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31]) total number of confs: 307 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237829 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237829 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237829/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237829 Building REAL300000237830 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237830' /scratch/stefan/7769818/working/building/REAL300000237830 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237830 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237830/0 /scratch/stefan/7769818/working/building/REAL300000237830 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/830 `/scratch/stefan/7769818/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)C=C2)C=N1) `REAL300000237830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237830 none O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 44, 44, 110, 110, 66, 110, 110, 110, 110, 110, 110, 1, 1, 6, 6, 6, 1, 1, 6, 6, 110, 110, 110, 1, 1, 6] 114 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 24, 25, 29, 30, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 38]) total number of confs: 366 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237830 none O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 114, 114, 62, 62, 110, 110, 62, 62, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 110, 110, 114, 114, 114, 110, 110, 62, 62, 1, 1, 1, 110, 110, 114] 114 rigid atoms, others: [33, 34, 35, 12, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 449 number of broken/clashed sets: 7 ./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: REAL300000237830 none O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 20, 20, 67, 67, 114, 114, 102, 114, 114, 114, 114, 114, 114, 6, 6, 1, 1, 1, 6, 6, 20, 20, 114, 114, 114, 6, 6, 1] 114 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 26, 27, 28] set([7, 8, 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: 314 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237830 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237830 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237830/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237830 Building REAL300000237831 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237831' /scratch/stefan/7769818/working/building/REAL300000237831 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237831 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237831/0 /scratch/stefan/7769818/working/building/REAL300000237831 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/831 `/scratch/stefan/7769818/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1) `REAL300000237831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237831 none O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 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, 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 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, 81, 81, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 201, 81, 81, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 19, 20, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 350 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237831 none O=C([O-])C1=C(F)C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 11, 11, 82, 82, 201, 201, 104, 201, 201, 201, 201, 201, 198, 1, 1, 1, 11, 11, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 29, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28]) total number of confs: 678 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237831 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237831 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237831/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237831 Building REAL300000237832 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237832' /scratch/stefan/7769818/working/building/REAL300000237832 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237832 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237832/0 /scratch/stefan/7769818/working/building/REAL300000237832 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/832 `/scratch/stefan/7769818/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1Cl) `REAL300000237832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237832 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 164, 80, 53, 80, 80, 30, 30, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 80, 80, 80, 201, 201, 80, 80, 30, 30, 1, 1, 1, 80] 201 rigid atoms, others: [32, 33, 34, 11, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 634 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237832 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 27, 40, 7, 1, 1, 1, 1, 1, 1, 5, 5, 26, 26, 80, 80, 37, 80, 80, 80, 80, 80, 80, 1, 1, 1, 27, 27, 1, 1, 5, 5, 80, 80, 80, 1] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 23, 24, 25, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 396 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237832 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237832 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237832/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237832 Building REAL300000237833 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237833' /scratch/stefan/7769818/working/building/REAL300000237833 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237833 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237833/0 /scratch/stefan/7769818/working/building/REAL300000237833 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/833 `/scratch/stefan/7769818/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC=C1C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1) `REAL300000237833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237833 none O=C([O-])C1=CC=CC=C1C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 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, 7, 7, 7, 7, 7, 7, 3, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 5, 4, 4, 3, 4, 4, 1, 1, 1, 1, 1, 1, 6, 6, 47, 47, 173, 173, 69, 173, 173, 173, 173, 173, 173, 1, 1, 4, 3, 4, 4, 1, 1, 6, 6, 173, 173, 173, 1, 1] 201 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 40, 41, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 621 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237833 none O=C([O-])C1=CC=CC=C1C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 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, 7, 7, 7, 7, 7, 7, 3, 7, 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 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, 161, 201, 201, 140, 140, 173, 173, 91, 91, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 173, 173, 201, 201, 201, 201, 173, 173, 91, 91, 1, 1, 1, 173, 173] 201 rigid atoms, others: [37, 38, 39, 15, 17, 18, 19, 20, 21, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41]) total number of confs: 721 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: REAL300000237833 none O=C([O-])C1=CC=CC=C1C1=CC=C(C=CC(=O)C2=CC=C([N+](=O)[O-])C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 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, 7, 7, 7, 7, 7, 7, 3, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 17, 17, 87, 87, 201, 201, 138, 201, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 1, 4, 4, 17, 17, 201, 201, 201, 4, 4] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 2, 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]) total number of confs: 620 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237833 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237833 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237833/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237833 Building REAL300000237834 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237834' /scratch/stefan/7769818/working/building/REAL300000237834 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237834 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237834/0 /scratch/stefan/7769818/working/building/REAL300000237834 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/834 `/scratch/stefan/7769818/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F) `REAL300000237834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237834 none COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F 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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 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, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 97, 97, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 201, 201, 201, 201, 97, 97, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 13, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 386 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237834 none COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CC=C([N+](=O)[O-])C=C1F 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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 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, 7, 7, 3, 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 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, 11, 11, 79, 79, 201, 201, 178, 201, 201, 201, 201, 201, 201, 3, 3, 3, 1, 1, 1, 11, 11, 201, 201, 201] 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]) total number of confs: 476 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237834 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237834 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237834/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237834 Building REAL300000237835 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237835' /scratch/stefan/7769818/working/building/REAL300000237835 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237835 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237835/0 /scratch/stefan/7769818/working/building/REAL300000237835 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/835 `/scratch/stefan/7769818/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)C(F)=CC=C2S1) `REAL300000237835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237835 none O=C([O-])C1=CC2=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 145, 145, 145, 71, 71, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 145, 145, 145, 145, 145, 145, 145, 71, 71, 1, 1, 1, 145, 145] 145 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 274 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237835 none O=C([O-])C1=CC2=C(C=CC(=O)C3=CC=C([N+](=O)[O-])C=C3F)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 9, 65, 65, 145, 145, 65, 145, 145, 145, 145, 145, 145, 1, 1, 1, 1, 1, 1, 1, 9, 9, 145, 145, 145, 1, 1] 145 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 33, 21, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31]) total number of confs: 575 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237835 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237835 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237835/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237835 Building REAL300000237836 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237836' /scratch/stefan/7769818/working/building/REAL300000237836 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237836 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237836/0 /scratch/stefan/7769818/working/building/REAL300000237836 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/836 `/scratch/stefan/7769818/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1OCC(=O)[O-]) `REAL300000237836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237836 none COC1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 15, 15, 9, 1, 9, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 39, 39, 39, 39, 133, 201, 201, 201, 67, 67, 67, 39, 15, 15, 1, 5, 5, 2, 5, 5, 39, 39, 201, 201] 201 rigid atoms, others: [34, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 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, 41, 42, 43]) total number of confs: 568 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237836 none COC1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 15, 15, 9, 5, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 133, 201, 201, 201, 67, 67, 67, 39, 15, 15, 5, 1, 1, 1, 1, 1, 39, 39, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43]) total number of confs: 555 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: REAL300000237836 none COC1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 9, 17, 19, 19, 3, 3, 3, 1, 5, 5, 39, 39, 39, 39, 39, 39, 1, 1, 17, 17] 201 rigid atoms, others: [1, 2, 3, 4, 5, 40, 41, 20, 21, 22, 23, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237836 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237836 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237836/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237836 Building REAL300000237837 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237837' /scratch/stefan/7769818/working/building/REAL300000237837 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237837 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237837/0 /scratch/stefan/7769818/working/building/REAL300000237837 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/837 `/scratch/stefan/7769818/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1) `REAL300000237837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237837 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 7, 7, 7, 7, 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: [85, 85, 85, 70, 85, 85, 70, 70, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 85, 85, 85, 85, 70, 70, 1, 6, 6, 2, 6, 6, 85, 85] 95 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 285 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237837 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 95, 95, 95, 95, 22, 6, 22, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 95, 6, 1, 1, 1, 1, 1, 95, 95] 95 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20, 21, 29, 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, 34, 35]) total number of confs: 237 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: REAL300000237837 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 82, 82, 82, 82, 82, 92, 92, 92, 92, 92, 1, 1, 1, 1, 6, 6, 82, 92, 92, 92, 92, 92, 1, 1] 92 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237837 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237837 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237837/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237837 Building REAL300000237838 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237838' /scratch/stefan/7769818/working/building/REAL300000237838 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237838 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237838/0 /scratch/stefan/7769818/working/building/REAL300000237838 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/838 `/scratch/stefan/7769818/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1) `REAL300000237838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237838 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 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: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 126, 74, 73, 74, 74, 27, 27, 11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 74, 74, 201, 201, 74, 74, 27, 27, 1, 5, 5, 1, 5, 5, 74, 74] 201 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 659 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237838 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 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: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 127, 77, 77, 77, 77, 29, 29, 13, 5, 13, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 77, 77, 201, 201, 77, 77, 29, 29, 5, 1, 1, 1, 1, 1, 77, 77] 201 rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 642 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: REAL300000237838 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 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: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 9, 14, 3, 1, 1, 1, 1, 1, 1, 5, 5, 23, 23, 74, 74, 74, 74, 74, 77, 77, 74, 77, 77, 1, 1, 10, 10, 1, 1, 5, 5, 74, 77, 77, 74, 77, 77, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 24, 25, 38, 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]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237838 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237838 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237838/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237838 Building REAL300000237839 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237839' /scratch/stefan/7769818/working/building/REAL300000237839 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237839 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237839/0 /scratch/stefan/7769818/working/building/REAL300000237839 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/839 `/scratch/stefan/7769818/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1) `REAL300000237839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237839 none O=C([O-])CCOC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 200, 199, 171, 96, 95, 96, 96, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 96, 96, 200, 200, 199, 199, 96, 96, 33, 33, 1, 5, 5, 1, 5, 5, 96, 96] 201 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 495 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237839 none O=C([O-])CCOC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 200, 200, 172, 102, 102, 102, 102, 36, 36, 15, 5, 15, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 102, 102, 201, 201, 200, 200, 102, 102, 36, 36, 5, 1, 1, 1, 1, 1, 102, 102] 201 rigid atoms, others: [36, 37, 38, 39, 40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 484 number of broken/clashed sets: 7 ./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: REAL300000237839 none O=C([O-])CCOC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 11, 15, 9, 3, 1, 1, 1, 1, 1, 1, 5, 5, 25, 25, 96, 96, 96, 96, 96, 102, 102, 98, 102, 102, 1, 1, 10, 10, 10, 10, 1, 1, 5, 5, 96, 102, 102, 98, 102, 102, 1, 1] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 41, 25, 26, 42, 31] set([0, 1, 2, 3, 4, 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: 230 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237839 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237839 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237839/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237839 Building REAL300000237840 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237840' /scratch/stefan/7769818/working/building/REAL300000237840 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237840 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237840/0 /scratch/stefan/7769818/working/building/REAL300000237840 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/840 `/scratch/stefan/7769818/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300000237840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237840 none CC(OC1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 167, 73, 73, 73, 73, 73, 40, 40, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 73, 197, 198, 198, 197, 197, 197, 197, 73, 73, 73, 40, 40, 1, 5, 5, 2, 5, 5, 73] 201 rigid atoms, others: [36, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 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: 492 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237840 none CC(OC1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 174, 84, 84, 84, 84, 84, 50, 50, 20, 5, 20, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 84, 201, 201, 201, 201, 201, 201, 201, 84, 84, 84, 50, 50, 5, 1, 1, 1, 1, 1, 84] 201 rigid atoms, others: [37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 487 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: REAL300000237840 none CC(OC1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 9, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 73, 73, 73, 73, 73, 84, 84, 73, 84, 84, 1, 20, 24, 24, 20, 20, 20, 20, 1, 1, 1, 5, 5, 73, 84, 84, 80, 84, 84, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 42, 23, 31] set([0, 1, 9, 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, 41]) total number of confs: 254 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237840 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237840 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237840/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237840 Building REAL300000237841 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237841' /scratch/stefan/7769818/working/building/REAL300000237841 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237841 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237841/0 /scratch/stefan/7769818/working/building/REAL300000237841 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/841 `/scratch/stefan/7769818/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1) `REAL300000237841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237841 none O=C([O-])CCOC1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 186, 46, 46, 46, 46, 46, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 46, 201, 201, 201, 201, 46, 46, 46, 19, 19, 1, 5, 5, 2, 5, 5, 46] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 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: 356 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237841 none O=C([O-])CCOC1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 186, 46, 46, 46, 46, 46, 19, 19, 9, 5, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 46, 201, 201, 201, 201, 46, 46, 46, 19, 19, 5, 1, 1, 1, 1, 1, 46] 201 rigid atoms, others: [37, 38, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 342 number of broken/clashed sets: 6 ./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: REAL300000237841 none O=C([O-])CCOC1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 14, 21, 14, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 19, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 14, 14, 14, 14, 1, 1, 1, 5, 5, 46, 46, 46, 46, 46, 46, 1] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 26, 42, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 148 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237841 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237841 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237841/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237841 Building REAL300000237842 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237842' /scratch/stefan/7769818/working/building/REAL300000237842 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237842 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237842/0 /scratch/stefan/7769818/working/building/REAL300000237842 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/842 `/scratch/stefan/7769818/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)O2)C=C1) `REAL300000237842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237842 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 12, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 101, 201, 201, 101, 101, 101, 101, 71, 71, 27, 5, 27, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 101, 201, 201, 201, 201, 101, 101, 71, 71, 5, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [36, 37, 38, 39, 40, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 832 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237842 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 12, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 6, 6, 1, 1, 1, 1, 1, 1, 10, 10, 22, 23, 83, 83, 83, 83, 83, 101, 101, 99, 101, 101, 1, 6, 6, 6, 6, 1, 1, 10, 10, 83, 101, 101, 99, 101, 101, 6, 6] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 26, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 198 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237842 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 12, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [185, 170, 185, 83, 185, 185, 83, 83, 83, 83, 46, 46, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 83, 185, 185, 185, 185, 83, 83, 46, 46, 1, 5, 5, 2, 5, 5, 185, 185] 201 rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 796 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: REAL300000237842 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 12, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 27, 27, 63, 63, 195, 195, 195, 195, 195, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 7, 7, 27, 27, 195, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 42, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237842 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237842 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237842/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237842 Building REAL300000237843 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237843' /scratch/stefan/7769818/working/building/REAL300000237843 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237843 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237843/0 /scratch/stefan/7769818/working/building/REAL300000237843 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/843 `/scratch/stefan/7769818/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1) `REAL300000237843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237843 none O=C([O-])COC1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 149, 60, 60, 60, 60, 60, 35, 35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 60, 194, 194, 60, 60, 60, 35, 35, 1, 5, 5, 2, 5, 5, 60] 201 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 526 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237843 none O=C([O-])COC1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 157, 70, 70, 70, 70, 70, 43, 43, 19, 5, 19, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 70, 201, 201, 70, 70, 70, 43, 43, 5, 1, 1, 1, 1, 1, 70] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39]) total number of confs: 530 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: REAL300000237843 none O=C([O-])COC1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 16, 23, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 60, 60, 60, 60, 60, 70, 70, 60, 70, 70, 1, 16, 16, 1, 1, 1, 5, 5, 60, 70, 70, 67, 70, 70, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 39, 25, 28, 29, 30] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 222 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237843 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237843 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237843/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237843 Building REAL300000237844 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237844' /scratch/stefan/7769818/working/building/REAL300000237844 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237844 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237844/0 /scratch/stefan/7769818/working/building/REAL300000237844 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/844 `/scratch/stefan/7769818/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1) `REAL300000237844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237844 none O=C([O-])C(F)(F)OC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 7, 7, 7, 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, 117, 201, 201, 46, 45, 46, 46, 15, 15, 9, 1, 9, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 46, 46, 46, 46, 15, 15, 1, 5, 5, 1, 5, 5, 46, 46] 201 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 640 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237844 none O=C([O-])C(F)(F)OC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 7, 7, 7, 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, 117, 201, 201, 46, 46, 46, 46, 15, 15, 9, 5, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 15, 15, 5, 1, 1, 1, 1, 1, 46, 46] 201 rigid atoms, others: [33, 34, 35, 36, 37, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 623 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: REAL300000237844 none O=C([O-])C(F)(F)OC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 7, 7, 7, 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: [21, 17, 21, 6, 17, 17, 1, 1, 1, 1, 1, 1, 5, 5, 20, 20, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 5, 5, 46, 46, 46, 46, 46, 46, 1, 1] 201 rigid atoms, others: [38, 6, 7, 8, 9, 10, 11, 39, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237844 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237844 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237844/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237844 Building REAL300000237845 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237845' /scratch/stefan/7769818/working/building/REAL300000237845 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237845 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237845/0 /scratch/stefan/7769818/working/building/REAL300000237845 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/845 `/scratch/stefan/7769818/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1) `REAL300000237845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237845 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 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, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 171, 171, 171, 171, 171, 171, 171, 171, 171, 171, 44, 44, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 171, 171, 186, 186, 186, 171, 44, 44, 1, 5, 5, 2, 5, 5, 171, 171] 201 rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 312 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237845 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 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, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 70, 28, 5, 28, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 70, 70, 5, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [36, 37, 38, 39, 40, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 354 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: REAL300000237845 none COC1=C2OC(C(=O)[O-])=CC2=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 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, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 11, 11, 55, 55, 171, 171, 171, 171, 171, 201, 201, 175, 201, 201, 1, 1, 3, 3, 3, 1, 11, 11, 171, 201, 201, 191, 201, 201, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 41, 27, 28, 42] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 440 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237845 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237845 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237845/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237845 Building REAL300000237846 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237846' /scratch/stefan/7769818/working/building/REAL300000237846 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237846 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237846/0 /scratch/stefan/7769818/working/building/REAL300000237846 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/846 `/scratch/stefan/7769818/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)N=N1) `REAL300000237846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237846 none O=C([O-])CN1C=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 120, 120, 120, 45, 45, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 120, 120, 197, 197, 120, 45, 45, 1, 5, 5, 2, 5, 5] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 651 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237846 none O=C([O-])CN1C=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 133, 133, 133, 61, 61, 23, 5, 23, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 133, 133, 201, 201, 133, 61, 61, 5, 1, 1, 1, 1, 1] 201 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]) total number of confs: 657 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: REAL300000237846 none O=C([O-])CN1C=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 10, 1, 1, 1, 1, 1, 13, 13, 46, 47, 120, 120, 120, 120, 120, 133, 133, 126, 133, 133, 1, 1, 6, 6, 1, 13, 13, 120, 133, 133, 126, 133, 133] 201 rigid atoms, others: [3, 4, 5, 6, 7, 22, 23, 26] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237846 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237846 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237846/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237846 Building REAL300000237847 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237847' /scratch/stefan/7769818/working/building/REAL300000237847 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237847 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237847/0 /scratch/stefan/7769818/working/building/REAL300000237847 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/847 `/scratch/stefan/7769818/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1) `REAL300000237847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237847 none O=C([O-])C1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 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: [167, 167, 167, 167, 167, 167, 167, 69, 69, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 167, 167, 167, 167, 69, 69, 1, 6, 6, 2, 6, 6, 167] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 329 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237847 none O=C([O-])C1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 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, 88, 88, 31, 6, 31, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 88, 88, 6, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 402 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: REAL300000237847 none O=C([O-])C1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 39, 39, 167, 167, 167, 167, 167, 201, 201, 198, 201, 201, 1, 1, 1, 1, 5, 5, 167, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 332 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237847 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237847 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237847/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237847 Building REAL300000237848 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237848' /scratch/stefan/7769818/working/building/REAL300000237848 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237848 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237848/0 /scratch/stefan/7769818/working/building/REAL300000237848 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/848 `/scratch/stefan/7769818/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1) `REAL300000237848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237848 none O=C([O-])C1=CSC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 176, 176, 176, 176, 176, 44, 44, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 176, 176, 44, 44, 1, 6, 6, 1, 6, 6, 176] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 292 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237848 none O=C([O-])C1=CSC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 61, 26, 6, 26, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 61, 61, 6, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 32, 22, 23, 24, 25, 26]) total number of confs: 347 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: REAL300000237848 none O=C([O-])C1=CSC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 78, 79, 176, 176, 176, 176, 176, 201, 201, 176, 201, 201, 1, 1, 13, 13, 176, 201, 201, 199, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 22, 23] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 503 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237848 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237848 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237848/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237848 Building REAL300000237849 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237849' /scratch/stefan/7769818/working/building/REAL300000237849 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237849 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237849/0 /scratch/stefan/7769818/working/building/REAL300000237849 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/849 `/scratch/stefan/7769818/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1OCCC(=O)[O-]) `REAL300000237849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237849 none COC1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 49, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 49, 49, 49, 49, 145, 180, 180, 201, 193, 91, 91, 91, 49, 17, 17, 1, 5, 5, 2, 5, 5, 49, 49, 180, 180, 180, 180] 201 rigid atoms, others: [35, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 618 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237849 none COC1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 49, 17, 17, 9, 5, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 145, 180, 180, 201, 193, 91, 91, 91, 49, 17, 17, 5, 1, 1, 1, 1, 1, 49, 49, 180, 180, 180, 180] 201 rigid atoms, others: [36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46]) total number of confs: 605 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: REAL300000237849 none COC1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 7, 13, 14, 21, 17, 3, 3, 3, 1, 5, 5, 49, 49, 49, 49, 49, 49, 1, 1, 13, 13, 13, 13] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 41, 42, 20, 21, 22, 23] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46]) total number of confs: 156 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237849 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237849 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237849/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237849 Building REAL300000237850 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237850' /scratch/stefan/7769818/working/building/REAL300000237850 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237850 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237850/0 /scratch/stefan/7769818/working/building/REAL300000237850 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/850 `/scratch/stefan/7769818/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C(Cl)=C1) `REAL300000237850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237850 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 167, 187, 82, 187, 187, 77, 77, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 187, 187, 187, 187, 187, 77, 77, 1, 6, 6, 1, 6, 6, 187] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 775 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237850 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 130, 201, 201, 122, 122, 30, 6, 30, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 122, 122, 6, 1, 1, 1, 1, 1, 201] 201 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]) total number of confs: 738 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: REAL300000237850 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 71, 71, 187, 187, 187, 187, 187, 201, 201, 187, 201, 201, 1, 1, 1, 1, 1, 9, 9, 187, 201, 201, 187, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 389 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237850 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237850 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237850/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237850 Building REAL300000237851 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237851' /scratch/stefan/7769818/working/building/REAL300000237851 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237851 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237851/0 /scratch/stefan/7769818/working/building/REAL300000237851 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/851 `/scratch/stefan/7769818/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1Cl) `REAL300000237851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237851 none O=C([O-])C1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 175, 175, 175, 175, 175, 175, 69, 69, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 175, 175, 175, 175, 175, 69, 69, 1, 5, 5, 1, 5, 5] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 323 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237851 none O=C([O-])C1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 112, 112, 29, 5, 29, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 112, 112, 5, 1, 1, 1, 1, 1] 201 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]) total number of confs: 429 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: REAL300000237851 none O=C([O-])C1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 9, 51, 51, 175, 175, 175, 175, 175, 201, 201, 175, 201, 201, 1, 1, 1, 1, 1, 9, 9, 175, 201, 201, 175, 201, 201] 201 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]) total number of confs: 411 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237851 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237851 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237851/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237851 Building REAL300000237852 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237852' /scratch/stefan/7769818/working/building/REAL300000237852 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237852 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237852/0 /scratch/stefan/7769818/working/building/REAL300000237852 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/852 `/scratch/stefan/7769818/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1O) `REAL300000237852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237852 none O=C([O-])C1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [172, 164, 172, 164, 164, 71, 71, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 164, 164, 164, 164, 164, 71, 71, 1, 6, 6, 1, 6, 6, 164, 164, 328] 402 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 678 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237852 none O=C([O-])C1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 97, 97, 29, 6, 29, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 97, 97, 6, 1, 1, 1, 1, 1, 201, 201, 402] 402 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36]) total number of confs: 805 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: REAL300000237852 none O=C([O-])C1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 5, 5, 37, 37, 164, 164, 164, 164, 164, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 5, 5, 164, 201, 201, 201, 201, 201, 1, 1, 2] 402 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 323 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237852 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237852 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237852/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237852 Building REAL300000237853 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237853' /scratch/stefan/7769818/working/building/REAL300000237853 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237853 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237853/0 /scratch/stefan/7769818/working/building/REAL300000237853 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/853 `/scratch/stefan/7769818/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1) `REAL300000237853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237853 none CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 182, 182, 182, 182, 182, 182, 182, 182, 74, 74, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 182, 182, 182, 182, 182, 182, 182, 182, 74, 74, 1, 5, 5, 2, 5, 5] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 337 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237853 none CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 113, 113, 29, 5, 29, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 113, 113, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 414 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: REAL300000237853 none CC1=CC(C)=C(C(=O)[O-])C=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 59, 59, 182, 182, 182, 182, 182, 201, 201, 182, 201, 201, 2, 2, 2, 1, 2, 2, 2, 1, 9, 9, 182, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 29] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 443 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237853 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237853 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237853/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237853 Building REAL300000237854 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237854' /scratch/stefan/7769818/working/building/REAL300000237854 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237854 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237854/0 /scratch/stefan/7769818/working/building/REAL300000237854 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/854 `/scratch/stefan/7769818/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300000237854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237854 none CC(OC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 153, 77, 71, 77, 77, 25, 25, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 77, 77, 201, 201, 201, 201, 201, 201, 201, 77, 77, 25, 25, 1, 5, 5, 1, 5, 5, 77, 77] 201 rigid atoms, others: [35, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 596 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237854 none CC(OC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 156, 80, 77, 80, 80, 27, 27, 14, 5, 14, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 80, 80, 201, 201, 201, 201, 201, 201, 201, 80, 80, 27, 27, 5, 1, 1, 1, 1, 1, 80, 80] 201 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]) total number of confs: 562 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: REAL300000237854 none CC(OC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 77, 77, 77, 77, 77, 80, 80, 77, 80, 80, 1, 1, 13, 17, 17, 13, 13, 13, 13, 1, 1, 5, 5, 77, 80, 80, 77, 80, 80, 1, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 41, 42, 22, 23, 31] set([0, 1, 8, 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, 40]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237854 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237854 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237854/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237854 Building REAL300000237855 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237855' /scratch/stefan/7769818/working/building/REAL300000237855 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237855 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237855/0 /scratch/stefan/7769818/working/building/REAL300000237855 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/855 `/scratch/stefan/7769818/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1) `REAL300000237855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237855 none O=C([O-])CCOC1=CC=CC=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 195, 201, 170, 72, 72, 72, 33, 72, 72, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 201, 201, 201, 201, 72, 72, 72, 72, 23, 23, 1, 5, 5, 1, 5, 5] 201 rigid atoms, others: [37, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 597 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237855 none O=C([O-])CCOC1=CC=CC=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 195, 201, 170, 72, 72, 72, 35, 72, 72, 23, 23, 9, 5, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 72, 72, 72, 72, 23, 23, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 581 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: REAL300000237855 none O=C([O-])CCOC1=CC=CC=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 42, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 30, 30, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 30, 30, 28, 28, 1, 1, 1, 1, 9, 9, 72, 72, 72, 72, 72, 72] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 282 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237855 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237855 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237855/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237855 Building REAL300000237856 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237856' /scratch/stefan/7769818/working/building/REAL300000237856 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237856 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237856/0 /scratch/stefan/7769818/working/building/REAL300000237856 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/856 `/scratch/stefan/7769818/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)[O-])=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1) `REAL300000237856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237856 none CN1N=CC(C(=O)[O-])=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 167, 167, 167, 174, 174, 59, 59, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 167, 167, 167, 167, 59, 59, 1, 6, 6, 2, 6, 6] 193 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 333 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237856 none CN1N=CC(C(=O)[O-])=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 193, 193, 193, 193, 193, 193, 87, 87, 28, 6, 28, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 193, 193, 193, 193, 87, 87, 6, 1, 1, 1, 1, 1] 193 rigid atoms, others: [32, 33, 34, 35, 17, 18, 19, 20, 21, 22, 23, 31] 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]) total number of confs: 375 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: REAL300000237856 none CN1N=CC(C(=O)[O-])=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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 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, 1, 1, 3, 3, 1, 1, 9, 9, 46, 46, 167, 167, 167, 167, 167, 193, 193, 172, 193, 193, 2, 2, 2, 1, 9, 9, 167, 193, 193, 189, 193, 193] 193 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 27] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 421 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237856 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237856 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237856/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237856 Building REAL300000237857 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237857' /scratch/stefan/7769818/working/building/REAL300000237857 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237857 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237857/0 /scratch/stefan/7769818/working/building/REAL300000237857 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/857 `/scratch/stefan/7769818/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1F) `REAL300000237857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237857 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 165, 179, 165, 165, 165, 66, 66, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 165, 165, 165, 165, 165, 66, 66, 1, 5, 5, 1, 5, 5, 165] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 372 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237857 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 96, 96, 29, 5, 29, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 96, 96, 5, 1, 1, 1, 1, 1, 201] 201 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]) total number of confs: 419 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: REAL300000237857 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 40, 40, 165, 165, 165, 165, 165, 201, 201, 197, 201, 201, 1, 1, 1, 1, 1, 5, 5, 165, 201, 201, 198, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25, 26] 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]) total number of confs: 339 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237857 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237857 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237857/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237857 Building REAL300000237858 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237858' /scratch/stefan/7769818/working/building/REAL300000237858 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237858 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237858/0 /scratch/stefan/7769818/working/building/REAL300000237858 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/858 `/scratch/stefan/7769818/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)O1) `REAL300000237858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237858 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 184, 195, 184, 115, 115, 115, 115, 46, 46, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 115, 184, 184, 115, 115, 46, 46, 1, 5, 5, 1, 5, 5] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 498 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237858 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 130, 130, 130, 130, 67, 67, 24, 5, 24, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 130, 201, 201, 130, 130, 67, 67, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 500 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: REAL300000237858 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 10, 19, 10, 1, 1, 1, 1, 1, 1, 12, 12, 31, 31, 115, 115, 115, 115, 115, 130, 130, 115, 130, 130, 1, 10, 10, 1, 1, 12, 12, 115, 130, 130, 115, 130, 130] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 24, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237858 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237858 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237858/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237858 Building REAL300000237859 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237859' /scratch/stefan/7769818/working/building/REAL300000237859 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237859 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237859/0 /scratch/stefan/7769818/working/building/REAL300000237859 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/859 `/scratch/stefan/7769818/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1C(=O)[O-]) `REAL300000237859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237859 none COC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1C(=O)[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.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 112, 112, 112, 112, 48, 48, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 112, 112, 112, 186, 186, 188, 188, 188, 112, 112, 48, 48, 1, 5, 5, 1, 5, 5, 112] 201 rigid atoms, others: [33, 8, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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: 674 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237859 none COC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1C(=O)[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.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 127, 127, 127, 127, 59, 59, 21, 5, 21, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 201, 201, 201, 201, 201, 127, 127, 59, 59, 5, 1, 1, 1, 1, 1, 127] 201 rigid atoms, others: [34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39]) total number of confs: 703 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: REAL300000237859 none COC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1C(=O)[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.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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 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, 27, 27, 112, 112, 112, 112, 112, 127, 127, 123, 127, 127, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 5, 5, 112, 127, 127, 123, 127, 127, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 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]) total number of confs: 219 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237859 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237859 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237859/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237859 Building REAL300000237860 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237860' /scratch/stefan/7769818/working/building/REAL300000237860 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237860 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237860/0 /scratch/stefan/7769818/working/building/REAL300000237860 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/860 `/scratch/stefan/7769818/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1) `REAL300000237860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237860 none O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=CN=NN2C2=CC=CC=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 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: [183, 183, 183, 183, 183, 183, 183, 183, 56, 56, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 183, 183, 183, 56, 56, 1, 6, 6, 2, 6, 6, 183] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 320 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237860 none O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=CN=NN2C2=CC=CC=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 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, 201, 201, 201, 201, 201, 80, 80, 31, 6, 31, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 80, 80, 6, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 378 number of broken/clashed sets: 6 ./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: REAL300000237860 none O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=CN=NN2C2=CC=CC=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 62, 62, 183, 183, 183, 183, 183, 201, 201, 201, 201, 201, 1, 1, 1, 11, 11, 183, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 24, 25, 26] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 338 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237860 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237860 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237860/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237860 Building REAL300000237861 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237861' /scratch/stefan/7769818/working/building/REAL300000237861 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237861 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237861/0 /scratch/stefan/7769818/working/building/REAL300000237861 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/861 `/scratch/stefan/7769818/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1) `REAL300000237861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237861 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 94, 94, 94, 94, 94, 151, 94, 94, 124, 124, 94, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 159, 159, 159, 94, 151, 151, 151, 94, 27, 27, 1, 5, 5, 1, 5, 5] 201 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 526 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237861 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 94, 94, 94, 94, 94, 151, 94, 94, 124, 124, 94, 27, 27, 9, 5, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 159, 159, 159, 94, 151, 151, 151, 94, 27, 27, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 514 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: REAL300000237861 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 3, 3, 1, 1, 1, 9, 9, 36, 36, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 4, 4, 4, 1, 3, 3, 3, 1, 9, 9, 94, 94, 94, 94, 94, 94] 201 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 11, 12, 13, 35, 31] set([0, 6, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237861 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237861 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237861/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237861 Building REAL300000237862 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237862' /scratch/stefan/7769818/working/building/REAL300000237862 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237862 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237862/0 /scratch/stefan/7769818/working/building/REAL300000237862 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/862 `/scratch/stefan/7769818/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1F) `REAL300000237862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237862 none O=C([O-])C1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [180, 171, 180, 171, 171, 71, 71, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 171, 171, 171, 171, 171, 71, 71, 1, 5, 5, 1, 5, 5, 171, 171] 201 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 365 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237862 none O=C([O-])C1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 91, 91, 26, 5, 26, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 91, 91, 5, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 396 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: REAL300000237862 none O=C([O-])C1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 5, 5, 37, 37, 171, 171, 171, 171, 171, 201, 201, 171, 201, 201, 1, 1, 1, 1, 1, 5, 5, 171, 201, 201, 171, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 403 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237862 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237862 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237862/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237862 Building REAL300000237863 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237863' /scratch/stefan/7769818/working/building/REAL300000237863 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237863 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237863/0 /scratch/stefan/7769818/working/building/REAL300000237863 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/863 `/scratch/stefan/7769818/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1) `REAL300000237863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237863 none O=C([O-])CC1=CC=C(C=CC(=O)C2=CN=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 170, 179, 70, 70, 170, 170, 70, 70, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 170, 170, 170, 170, 170, 170, 70, 70, 1, 6, 6, 1, 6, 6, 170, 170] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1002 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237863 none O=C([O-])CC1=CC=C(C=CC(=O)C2=CN=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 105, 105, 201, 201, 105, 105, 32, 6, 32, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 105, 105, 6, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 1107 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: REAL300000237863 none O=C([O-])CC1=CC=C(C=CC(=O)C2=CN=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 6, 6, 44, 44, 170, 170, 170, 170, 170, 201, 201, 170, 201, 201, 1, 1, 2, 2, 1, 1, 6, 6, 170, 201, 201, 170, 201, 201, 1, 1] 201 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: 426 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237863 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237863 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237863/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237863 Building REAL300000237864 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237864' /scratch/stefan/7769818/working/building/REAL300000237864 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237864 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237864/0 /scratch/stefan/7769818/working/building/REAL300000237864 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/864 `/scratch/stefan/7769818/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(Br)=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1) `REAL300000237864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237864 none O=C([O-])C1=CC(Br)=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 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: [170, 170, 170, 170, 170, 170, 170, 170, 70, 70, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 170, 170, 170, 70, 70, 1, 6, 6, 2, 6, 6, 170] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 333 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237864 none O=C([O-])C1=CC(Br)=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 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, 201, 201, 201, 201, 201, 90, 90, 27, 6, 27, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 90, 90, 6, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 401 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: REAL300000237864 none O=C([O-])C1=CC(Br)=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 37, 37, 170, 170, 170, 170, 170, 201, 201, 170, 201, 201, 1, 1, 1, 5, 5, 170, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 35, 24, 25, 26] 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]) total number of confs: 468 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237864 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237864 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237864/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237864 Building REAL300000237865 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237865' /scratch/stefan/7769818/working/building/REAL300000237865 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237865 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237865/0 /scratch/stefan/7769818/working/building/REAL300000237865 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/865 `/scratch/stefan/7769818/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)S1) `REAL300000237865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237865 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 181, 181, 181, 181, 181, 65, 65, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 181, 181, 181, 65, 65, 1, 6, 6, 1, 6, 6] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 319 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237865 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 96, 96, 31, 6, 31, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 96, 96, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27]) total number of confs: 387 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: REAL300000237865 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 10, 69, 69, 181, 181, 181, 181, 181, 201, 201, 181, 201, 201, 1, 1, 1, 10, 10, 175, 201, 201, 181, 201, 201] 201 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]) total number of confs: 429 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237865 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237865 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237865/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237865 Building REAL300000237866 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237866' /scratch/stefan/7769818/working/building/REAL300000237866 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237866 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237866/0 /scratch/stefan/7769818/working/building/REAL300000237866 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/866 `/scratch/stefan/7769818/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1) `REAL300000237866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237866 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [181, 173, 181, 169, 119, 74, 157, 157, 74, 74, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 157, 157, 171, 171, 157, 157, 74, 74, 1, 5, 5, 1, 5, 5, 157, 157] 201 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 800 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237866 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 165, 111, 201, 201, 111, 111, 29, 5, 29, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 111, 111, 5, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 866 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: REAL300000237866 none O=C([O-])C=CC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 3, 10, 3, 1, 1, 1, 1, 1, 1, 5, 5, 38, 38, 157, 157, 157, 157, 157, 201, 201, 157, 201, 201, 1, 1, 3, 3, 1, 1, 5, 5, 157, 201, 201, 157, 201, 201, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 24, 25, 38, 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]) total number of confs: 477 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237866 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237866 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237866/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237866 Building REAL300000237867 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237867' /scratch/stefan/7769818/working/building/REAL300000237867 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237867 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237867/0 /scratch/stefan/7769818/working/building/REAL300000237867 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/867 `/scratch/stefan/7769818/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1F) `REAL300000237867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237867 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 183, 190, 183, 183, 183, 183, 52, 52, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 183, 183, 183, 183, 52, 52, 1, 5, 5, 2, 5, 5, 183] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 345 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237867 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 70, 70, 23, 5, 23, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 70, 70, 5, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 366 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: REAL300000237867 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 48, 48, 183, 183, 183, 183, 183, 201, 201, 183, 201, 201, 1, 1, 1, 1, 11, 11, 183, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26] set([0, 2, 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: 417 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237867 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237867 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237867/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237867 Building REAL300000237868 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237868' /scratch/stefan/7769818/working/building/REAL300000237868 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237868 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237868/0 /scratch/stefan/7769818/working/building/REAL300000237868 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/868 `/scratch/stefan/7769818/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NNC2=CC=CC(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)=C21) `REAL300000237868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237868 none O=C([O-])C1=NNC2=CC=CC(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 116, 116, 116, 116, 116, 116, 45, 45, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 116, 116, 116, 116, 116, 45, 45, 1, 5, 5, 2, 5, 5] 128 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 222 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237868 none O=C([O-])C1=NNC2=CC=CC(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 62, 62, 21, 5, 21, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 128, 62, 62, 5, 1, 1, 1, 1, 1] 128 rigid atoms, others: [34, 35, 36, 37, 38, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 254 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: REAL300000237868 none O=C([O-])C1=NNC2=CC=CC(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 46, 46, 116, 116, 116, 116, 116, 128, 128, 117, 128, 128, 1, 1, 1, 1, 1, 9, 9, 116, 128, 128, 128, 128, 128] 128 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29, 30] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237868 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237868 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237868/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237868 Building REAL300000237869 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237869' /scratch/stefan/7769818/working/building/REAL300000237869 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237869 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237869/0 /scratch/stefan/7769818/working/building/REAL300000237869 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/869 `/scratch/stefan/7769818/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C(C2=CC=CC=C2)=N1) `REAL300000237869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237869 none O=C([O-])CN1C=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 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, 7] dock color type numbers: [2, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 15, 5, 5, 5, 5, 5, 21, 21, 50, 50, 147, 147, 147, 147, 147, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 5, 21, 21, 147, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 285 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237869 none O=C([O-])CN1C=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 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, 7] dock color type numbers: [2, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 99, 99, 99, 34, 34, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 99, 99, 147, 147, 99, 147, 147, 99, 197, 197, 99, 34, 34, 1, 5, 5, 1, 5, 5, 147, 147, 99, 147, 147] 201 rigid atoms, others: [35, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 901 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237869 none O=C([O-])CN1C=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 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, 7] dock color type numbers: [2, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 99, 99, 99, 34, 34, 12, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 99, 99, 147, 147, 99, 147, 147, 99, 197, 197, 99, 34, 34, 5, 1, 1, 1, 1, 1, 147, 147, 99, 147, 147] 201 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]) total number of confs: 893 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: REAL300000237869 none O=C([O-])CN1C=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 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, 7] dock color type numbers: [2, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 10, 1, 1, 1, 1, 1, 11, 11, 28, 29, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 1, 1, 5, 5, 1, 5, 5, 1, 6, 6, 1, 11, 11, 99, 99, 99, 99, 99, 99, 5, 5, 1, 5, 5] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 22, 23, 29] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237869 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237869 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237869/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237869 Building REAL300000237870 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237870' /scratch/stefan/7769818/working/building/REAL300000237870 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237870 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237870/0 /scratch/stefan/7769818/working/building/REAL300000237870 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/870 `/scratch/stefan/7769818/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)C=C2)C=C1) `REAL300000237870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237870 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [155, 153, 155, 131, 155, 155, 109, 109, 118, 118, 109, 109, 31, 6, 31, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 118, 118, 155, 155, 155, 155, 118, 118, 109, 109, 6, 1, 1, 1, 1, 1, 118, 118, 155, 155] 155 rigid atoms, others: [37, 38, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45]) total number of confs: 532 number of broken/clashed sets: 4 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237870 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 28, 28, 89, 89, 89, 89, 89, 119, 119, 95, 119, 119, 1, 1, 3, 3, 3, 3, 1, 1, 3, 3, 89, 119, 119, 95, 119, 119, 1, 1, 3, 3] 153 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 43, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 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, 44, 45]) total number of confs: 268 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237870 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [142, 132, 142, 106, 142, 142, 72, 72, 89, 89, 72, 72, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 89, 89, 142, 142, 142, 142, 89, 89, 72, 72, 1, 6, 6, 1, 6, 6, 89, 89, 142, 142] 155 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 568 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: REAL300000237870 none O=C([O-])C1=CC=C(C2=CC=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 6, 46, 46, 139, 139, 139, 139, 139, 153, 153, 140, 153, 153, 3, 3, 1, 1, 1, 1, 3, 3, 6, 6, 139, 153, 153, 140, 153, 153, 3, 3, 1, 1] 153 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 45, 28, 29, 30, 31] set([0, 2, 8, 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, 42, 43]) total number of confs: 306 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237870 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237870 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237870/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237870 Building REAL300000237871 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237871' /scratch/stefan/7769818/working/building/REAL300000237871 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237871 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237871/0 /scratch/stefan/7769818/working/building/REAL300000237871 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/871 `/scratch/stefan/7769818/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2NC=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)C2=C1) `REAL300000237871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237871 none O=C([O-])C1=CC=C2NC=C(C=CC(=O)C3=CN=NN3C3=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', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [185, 185, 185, 185, 185, 185, 185, 185, 185, 44, 44, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 185, 185, 185, 185, 185, 185, 44, 44, 1, 5, 5, 1, 5, 5, 185] 201 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237871 none O=C([O-])C1=CC=C2NC=C(C=CC(=O)C3=CN=NN3C3=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', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 58, 58, 21, 5, 21, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 58, 58, 5, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39]) total number of confs: 325 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: REAL300000237871 none O=C([O-])C1=CC=C2NC=C(C=CC(=O)C3=CN=NN3C3=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', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 62, 63, 185, 185, 185, 185, 185, 201, 201, 185, 201, 201, 1, 1, 1, 1, 1, 1, 11, 11, 185, 201, 201, 185, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 25, 26, 27, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 394 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237871 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237871 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237871/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237871 Building REAL300000237872 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237872' /scratch/stefan/7769818/working/building/REAL300000237872 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237872 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237872/0 /scratch/stefan/7769818/working/building/REAL300000237872 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/872 `/scratch/stefan/7769818/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=N1) `REAL300000237872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237872 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 157, 157, 157, 76, 76, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 157, 157, 157, 157, 76, 76, 1, 6, 6, 1, 6, 6, 157] 176 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 325 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237872 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 176, 176, 176, 176, 113, 113, 25, 6, 25, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 176, 176, 176, 176, 113, 113, 6, 1, 1, 1, 1, 1, 176] 176 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20, 21, 29, 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, 34]) total number of confs: 399 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: REAL300000237872 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 41, 41, 157, 157, 157, 157, 157, 176, 176, 176, 176, 176, 1, 1, 1, 1, 5, 5, 157, 176, 176, 176, 176, 176, 1] 176 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 284 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237872 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237872 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237872/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237872 Building REAL300000237873 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237873' /scratch/stefan/7769818/working/building/REAL300000237873 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237873 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237873/0 /scratch/stefan/7769818/working/building/REAL300000237873 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/873 `/scratch/stefan/7769818/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1O) `REAL300000237873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237873 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [183, 172, 183, 172, 172, 172, 79, 79, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 172, 172, 172, 172, 172, 79, 79, 1, 6, 6, 1, 6, 6, 172, 344] 402 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 721 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237873 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 127, 127, 34, 6, 34, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 127, 127, 6, 1, 1, 1, 1, 1, 201, 402] 402 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: 846 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: REAL300000237873 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 41, 41, 172, 172, 172, 172, 172, 201, 201, 172, 201, 201, 1, 1, 1, 1, 1, 5, 5, 172, 201, 201, 172, 201, 201, 1, 2] 402 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25, 26] 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, 36]) total number of confs: 413 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237873 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237873 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237873/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237873 Building REAL300000237874 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237874' /scratch/stefan/7769818/working/building/REAL300000237874 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237874 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237874/0 /scratch/stefan/7769818/working/building/REAL300000237874 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/874 `/scratch/stefan/7769818/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1C(=O)[O-]) `REAL300000237874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237874 none CC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 169, 68, 68, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 169, 169, 169, 179, 179, 169, 169, 169, 169, 169, 68, 68, 1, 6, 6, 2, 6, 6, 169] 201 rigid atoms, others: [32, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 367 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237874 none CC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 3, 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 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, 93, 93, 29, 6, 29, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 93, 6, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 392 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: REAL300000237874 none CC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 37, 37, 169, 169, 169, 169, 169, 201, 201, 186, 201, 201, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 5, 5, 169, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 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]) total number of confs: 395 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237874 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237874 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237874/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237874 Building REAL300000237875 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237875' /scratch/stefan/7769818/working/building/REAL300000237875 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237875 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237875/0 /scratch/stefan/7769818/working/building/REAL300000237875 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/875 `/scratch/stefan/7769818/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)SC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1) `REAL300000237875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237875 none O=C([O-])C1=C(Cl)SC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 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: [195, 190, 195, 190, 190, 190, 190, 27, 27, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 190, 27, 27, 1, 5, 5, 1, 5, 5, 190] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237875 none O=C([O-])C1=C(Cl)SC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 201, 201, 201, 201, 35, 35, 20, 5, 20, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 35, 35, 5, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 32, 23, 24, 25, 26]) total number of confs: 289 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: REAL300000237875 none O=C([O-])C1=C(Cl)SC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 62, 63, 190, 190, 190, 190, 190, 201, 201, 190, 201, 201, 1, 13, 13, 190, 201, 201, 190, 201, 201, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 23] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237875 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237875 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237875/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237875 Building REAL300000237876 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237876' /scratch/stefan/7769818/working/building/REAL300000237876 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237876 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237876/0 /scratch/stefan/7769818/working/building/REAL300000237876 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/876 `/scratch/stefan/7769818/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)O1) `REAL300000237876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237876 none CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 171, 171, 176, 176, 171, 70, 70, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 171, 171, 171, 171, 171, 70, 70, 1, 6, 6, 1, 6, 6] 197 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237876 none CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 199, 199, 199, 199, 199, 118, 118, 31, 6, 31, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 199, 118, 118, 6, 1, 1, 1, 1, 1] 199 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]) total number of confs: 417 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: REAL300000237876 none CC1=C(C(=O)[O-])C=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 57, 57, 171, 171, 171, 171, 171, 197, 197, 171, 197, 197, 1, 2, 2, 2, 1, 11, 11, 171, 197, 197, 179, 197, 197] 197 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 23, 27] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 442 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237876 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237876 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237876/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237876 Building REAL300000237877 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237877' /scratch/stefan/7769818/working/building/REAL300000237877 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237877 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237877/0 /scratch/stefan/7769818/working/building/REAL300000237877 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/877 `/scratch/stefan/7769818/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1) `REAL300000237877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237877 none CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 194, 194, 194, 194, 194, 194, 194, 73, 73, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 194, 194, 194, 194, 73, 73, 1, 6, 6, 1, 6, 6] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 356 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237877 none CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 109, 109, 33, 6, 33, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 109, 109, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 17, 18, 19, 20, 21, 22, 23, 31] 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]) total number of confs: 420 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: REAL300000237877 none CN1N=C(C(=O)[O-])C=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 74, 74, 194, 194, 194, 194, 194, 201, 201, 194, 201, 201, 2, 2, 2, 1, 10, 10, 194, 201, 201, 194, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237877 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237877 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237877/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237877 Building REAL300000237878 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237878' /scratch/stefan/7769818/working/building/REAL300000237878 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237878 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237878/0 /scratch/stefan/7769818/working/building/REAL300000237878 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/878 `/scratch/stefan/7769818/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1) `REAL300000237878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237878 none O=C([O-])C1=CN=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 166, 166, 166, 166, 166, 166, 71, 71, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 166, 166, 166, 71, 71, 1, 6, 6, 1, 6, 6, 166] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 327 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237878 none O=C([O-])C1=CN=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 96, 96, 32, 6, 32, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 96, 96, 6, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 34]) total number of confs: 408 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: REAL300000237878 none O=C([O-])C1=CN=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 39, 39, 166, 166, 166, 166, 166, 201, 201, 197, 201, 201, 1, 1, 1, 6, 6, 166, 201, 201, 187, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 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]) total number of confs: 342 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237878 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237878 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237878/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237878 Building REAL300000237879 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237879' /scratch/stefan/7769818/working/building/REAL300000237879 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237879 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237879/0 /scratch/stefan/7769818/working/building/REAL300000237879 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/879 `/scratch/stefan/7769818/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=COC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1) `REAL300000237879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237879 none O=C([O-])C1=COC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 153, 153, 153, 72, 72, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 153, 153, 72, 72, 1, 6, 6, 1, 6, 6, 153] 181 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237879 none O=C([O-])C1=COC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [181, 181, 181, 181, 181, 181, 109, 109, 28, 6, 28, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 181, 181, 109, 109, 6, 1, 1, 1, 1, 1, 181] 181 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 32, 22, 23, 24, 25, 26]) total number of confs: 381 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: REAL300000237879 none O=C([O-])C1=COC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 60, 61, 153, 153, 153, 153, 153, 181, 181, 153, 181, 181, 1, 1, 10, 10, 153, 181, 181, 160, 181, 181, 1] 181 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 22, 23] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 425 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237879 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237879 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237879/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237879 Building REAL300000237880 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237880' /scratch/stefan/7769818/working/building/REAL300000237880 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237880 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237880/0 /scratch/stefan/7769818/working/building/REAL300000237880 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/880 `/scratch/stefan/7769818/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1) `REAL300000237880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237880 none COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CN=NN1C1=CC=CC=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 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, 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, 7, 7, 7] 0 hydrogens 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, 189, 189, 189, 189, 189, 189, 189, 189, 40, 40, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 201, 201, 201, 189, 189, 189, 40, 40, 1, 5, 5, 1, 5, 5] 201 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 323 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237880 none COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CN=NN1C1=CC=CC=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 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, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 51, 51, 17, 5, 17, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 51, 51, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 327 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: REAL300000237880 none COC1=CC=C(C(=O)[O-])C=C1C=CC(=O)C1=CN=NN1C1=CC=CC=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 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, 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, 7, 7, 7] 0 hydrogens 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, 9, 9, 47, 47, 189, 189, 189, 189, 189, 201, 201, 189, 201, 201, 3, 3, 3, 1, 1, 1, 9, 9, 189, 201, 201, 189, 201, 201] 201 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]) total number of confs: 356 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237880 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237880 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237880/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237880 Building REAL300000237881 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237881' /scratch/stefan/7769818/working/building/REAL300000237881 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237881 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237881/0 /scratch/stefan/7769818/working/building/REAL300000237881 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/881 `/scratch/stefan/7769818/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2SC=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)C2=C1) `REAL300000237881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237881 none O=C([O-])C1=CC=C2SC=C(C=CC(=O)C3=CN=NN3C3=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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 14, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 7, 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: [182, 182, 182, 182, 182, 182, 182, 182, 182, 60, 60, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 182, 182, 182, 182, 182, 60, 60, 1, 5, 5, 1, 5, 5, 182] 201 rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 305 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237881 none O=C([O-])C1=CC=C2SC=C(C=CC(=O)C3=CN=NN3C3=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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 14, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 7, 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, 201, 201, 73, 73, 23, 5, 23, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 73, 73, 5, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 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, 38]) total number of confs: 346 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: REAL300000237881 none O=C([O-])C1=CC=C2SC=C(C=CC(=O)C3=CN=NN3C3=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', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 14, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 55, 55, 182, 182, 182, 182, 182, 201, 201, 182, 201, 201, 1, 1, 1, 1, 1, 9, 10, 182, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 38, 25, 26, 27, 28, 29] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 434 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237881 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237881 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237881/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237881 Building REAL300000237882 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237882' /scratch/stefan/7769818/working/building/REAL300000237882 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237882 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237882/0 /scratch/stefan/7769818/working/building/REAL300000237882 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/882 `/scratch/stefan/7769818/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Br)C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1) `REAL300000237882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237882 none O=C([O-])C1=CC=C(Br)C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 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: [173, 173, 173, 173, 173, 173, 173, 173, 63, 63, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 173, 173, 173, 63, 63, 1, 5, 5, 1, 5, 5, 173] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 314 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237882 none O=C([O-])C1=CC=C(Br)C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 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, 201, 201, 201, 201, 201, 100, 100, 28, 5, 28, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 100, 100, 5, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 406 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: REAL300000237882 none O=C([O-])C1=CC=C(Br)C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 58, 58, 173, 173, 173, 173, 173, 201, 201, 173, 201, 201, 1, 1, 1, 9, 9, 173, 201, 201, 173, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 24, 25, 26] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 419 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237882 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237882 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237882/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237882 Building REAL300000237883 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237883' /scratch/stefan/7769818/working/building/REAL300000237883 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237883 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237883/0 /scratch/stefan/7769818/working/building/REAL300000237883 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/883 `/scratch/stefan/7769818/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C([N+](=O)[O-])=C1) `REAL300000237883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237883 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 134, 165, 134, 165, 165, 84, 84, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 165, 165, 165, 165, 165, 165, 161, 84, 84, 1, 6, 6, 2, 6, 6, 165] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 563 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237883 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 201, 199, 201, 201, 145, 145, 30, 6, 30, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 199, 145, 145, 6, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37]) total number of confs: 477 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: REAL300000237883 none O=C([O-])C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 39, 39, 165, 165, 165, 165, 165, 201, 201, 201, 201, 201, 1, 1, 2, 2, 1, 1, 1, 7, 7, 165, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 26, 27, 28, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237883 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237883 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237883/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237883 Building REAL300000237884 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237884' /scratch/stefan/7769818/working/building/REAL300000237884 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237884 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237884/0 /scratch/stefan/7769818/working/building/REAL300000237884 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/884 `/scratch/stefan/7769818/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1) `REAL300000237884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237884 none O=C([O-])CC1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 192, 194, 109, 109, 100, 109, 109, 47, 47, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 109, 192, 192, 109, 109, 109, 47, 47, 1, 5, 5, 1, 5, 5, 109] 201 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 774 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237884 none O=C([O-])CC1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 118, 118, 108, 118, 118, 54, 54, 19, 5, 19, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 118, 201, 201, 118, 118, 118, 54, 54, 5, 1, 1, 1, 1, 1, 118] 201 rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 783 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: REAL300000237884 none O=C([O-])CC1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 29, 29, 109, 109, 109, 109, 109, 118, 118, 109, 118, 118, 1, 2, 2, 1, 1, 1, 5, 5, 109, 118, 118, 109, 118, 118, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 38, 24, 27, 28, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 231 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237884 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237884 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237884/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237884 Building REAL300000237885 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237885' /scratch/stefan/7769818/working/building/REAL300000237885 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237885 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237885/0 /scratch/stefan/7769818/working/building/REAL300000237885 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/885 `/scratch/stefan/7769818/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1C(=O)[O-]) `REAL300000237885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237885 none COC1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 118, 118, 118, 47, 47, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 118, 118, 118, 118, 173, 173, 187, 187, 187, 118, 47, 47, 1, 5, 5, 1, 5, 5, 118, 118] 201 rigid atoms, others: [32, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 589 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237885 none COC1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 149, 149, 149, 66, 66, 25, 5, 25, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 201, 201, 201, 201, 201, 149, 66, 66, 5, 1, 1, 1, 1, 1, 149, 149] 201 rigid atoms, others: [33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 604 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: REAL300000237885 none COC1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 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, 3, 7, 7, 7, 7, 7, 7, 3, 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 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, 5, 5, 30, 30, 118, 118, 118, 118, 118, 149, 149, 118, 149, 149, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 5, 5, 118, 149, 149, 121, 149, 149, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 20, 21, 22, 23, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 338 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237885 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237885 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237885/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237885 Building REAL300000237886 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237886' /scratch/stefan/7769818/working/building/REAL300000237886 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237886 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237886/0 /scratch/stefan/7769818/working/building/REAL300000237886 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/886 `/scratch/stefan/7769818/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C(F)=C1) `REAL300000237886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237886 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [126, 105, 126, 102, 126, 126, 126, 77, 77, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 126, 126, 126, 126, 77, 77, 1, 6, 6, 1, 6, 6, 126] 140 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 424 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237886 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 134, 140, 133, 140, 140, 140, 106, 106, 30, 6, 30, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 106, 106, 6, 1, 1, 1, 1, 1, 140] 140 rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 381 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: REAL300000237886 none O=C([O-])C1=CC(F)=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 51, 51, 126, 126, 126, 126, 126, 140, 140, 126, 140, 140, 1, 1, 1, 1, 8, 8, 126, 140, 140, 126, 140, 140, 1] 140 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26] set([0, 2, 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: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237886 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237886 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237886/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237886 Building REAL300000237887 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237887' /scratch/stefan/7769818/working/building/REAL300000237887 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237887 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237887/0 /scratch/stefan/7769818/working/building/REAL300000237887 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/887 `/scratch/stefan/7769818/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1F) `REAL300000237887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237887 none O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 182, 189, 182, 182, 182, 182, 182, 48, 48, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 182, 182, 182, 182, 48, 48, 1, 5, 5, 2, 5, 5] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 328 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237887 none O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 65, 65, 24, 5, 24, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 65, 65, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 17, 18, 19, 20, 21, 22, 23, 31] 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]) total number of confs: 345 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: REAL300000237887 none O=C([O-])C1=CC=C(F)C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 59, 59, 182, 182, 182, 182, 182, 201, 201, 182, 201, 201, 1, 1, 1, 1, 11, 11, 182, 201, 201, 201, 201, 201] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 439 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237887 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237887 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237887/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237887 Building REAL300000237888 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237888' /scratch/stefan/7769818/working/building/REAL300000237888 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237888 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237888/0 /scratch/stefan/7769818/working/building/REAL300000237888 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/888 `/scratch/stefan/7769818/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CS1) `REAL300000237888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237888 none O=C([O-])C1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 179, 179, 179, 179, 87, 87, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 179, 179, 179, 87, 87, 1, 6, 6, 1, 6, 6, 179] 201 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 357 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237888 none O=C([O-])C1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 123, 123, 33, 6, 33, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 123, 123, 6, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 21, 22, 23, 24, 25, 26]) total number of confs: 439 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: REAL300000237888 none O=C([O-])C1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 6, 6, 49, 49, 179, 179, 179, 179, 179, 201, 201, 179, 201, 201, 1, 1, 1, 6, 6, 179, 201, 201, 179, 201, 201, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 393 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237888 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237888 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237888/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237888 Building REAL300000237889 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237889' /scratch/stefan/7769818/working/building/REAL300000237889 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237889 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237889/0 /scratch/stefan/7769818/working/building/REAL300000237889 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/889 `/scratch/stefan/7769818/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1OCC(=O)[O-]) `REAL300000237889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237889 none CCOC1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 37, 37, 13, 13, 9, 1, 9, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 37, 37, 37, 37, 136, 201, 201, 201, 67, 67, 67, 67, 67, 37, 13, 13, 1, 5, 5, 1, 5, 5, 37, 37, 201, 201] 201 rigid atoms, others: [37, 8, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 645 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237889 none CCOC1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 37, 37, 13, 13, 9, 5, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 136, 201, 201, 201, 67, 67, 67, 67, 67, 37, 13, 13, 5, 1, 1, 1, 1, 1, 37, 37, 201, 201] 201 rigid atoms, others: [38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46]) total number of confs: 633 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: REAL300000237889 none CCOC1=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 5, 5, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 7, 15, 18, 18, 3, 3, 3, 3, 3, 1, 5, 5, 37, 37, 37, 37, 37, 37, 1, 1, 15, 15] 201 rigid atoms, others: [34, 3, 4, 5, 6, 43, 44, 2, 21, 22, 23, 24] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237889 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237889 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237889/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237889 Building REAL300000237890 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237890' /scratch/stefan/7769818/working/building/REAL300000237890 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237890 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237890/0 /scratch/stefan/7769818/working/building/REAL300000237890 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/890 `/scratch/stefan/7769818/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1F) `REAL300000237890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237890 none O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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: [125, 82, 125, 82, 115, 115, 115, 82, 82, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 115, 115, 115, 115, 82, 82, 1, 6, 6, 2, 6, 6, 115] 149 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 519 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237890 none O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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, 119, 149, 119, 149, 149, 149, 119, 119, 30, 6, 30, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 119, 119, 6, 1, 1, 1, 1, 1, 149] 149 rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 561 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: REAL300000237890 none O=C([O-])C1=C(F)C=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 21, 21, 116, 116, 116, 116, 116, 150, 150, 148, 150, 150, 1, 1, 1, 1, 3, 3, 116, 150, 150, 150, 150, 150, 1] 150 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26] set([0, 2, 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: 245 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237890 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237890 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237890/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237890 Building REAL300000237891 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237891' /scratch/stefan/7769818/working/building/REAL300000237891 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237891 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237891/0 /scratch/stefan/7769818/working/building/REAL300000237891 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/891 `/scratch/stefan/7769818/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)O2)N1) `REAL300000237891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237891 none O=C([O-])C1=CC2=C(C=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)O2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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: [139, 139, 139, 139, 139, 139, 139, 139, 64, 64, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 139, 139, 139, 139, 64, 64, 1, 6, 6, 2, 6, 6, 139] 158 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 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.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237891 none O=C([O-])C1=CC2=C(C=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)O2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 158, 158, 158, 158, 158, 99, 99, 26, 6, 26, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 99, 99, 6, 1, 1, 1, 1, 1, 158] 158 rigid atoms, others: [32, 33, 34, 35, 17, 18, 19, 20, 21, 22, 23, 31] 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, 36]) total number of confs: 333 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: REAL300000237891 none O=C([O-])C1=CC2=C(C=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)O2)N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 55, 55, 139, 139, 139, 139, 139, 158, 158, 139, 158, 158, 1, 1, 1, 1, 10, 10, 139, 158, 158, 158, 158, 158, 1] 158 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 36] set([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: 376 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237891 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237891 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237891/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237891 Building REAL300000237892 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237892' /scratch/stefan/7769818/working/building/REAL300000237892 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237892 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237892/0 /scratch/stefan/7769818/working/building/REAL300000237892 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/892 `/scratch/stefan/7769818/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)=CC=C2O1) `REAL300000237892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237892 none O=C([O-])C1=CC2=CC(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 169, 169, 169, 169, 68, 68, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 169, 169, 169, 169, 169, 169, 68, 68, 1, 6, 6, 2, 6, 6, 169, 169] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 331 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237892 none O=C([O-])C1=CC2=CC(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 94, 94, 32, 6, 32, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 94, 94, 6, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 409 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: REAL300000237892 none O=C([O-])C1=CC2=CC(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 40, 40, 169, 169, 169, 169, 169, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 5, 5, 169, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 38, 23, 24, 25, 26, 27, 28, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 323 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237892 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237892 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237892/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237892 Building REAL300000237893 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237893' /scratch/stefan/7769818/working/building/REAL300000237893 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237893 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237893/0 /scratch/stefan/7769818/working/building/REAL300000237893 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/893 `/scratch/stefan/7769818/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)=CC=CN12) `REAL300000237893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237893 none O=C([O-])C1=CN=C2C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 182, 182, 182, 182, 182, 59, 59, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 182, 182, 182, 182, 182, 59, 59, 1, 5, 5, 1, 5, 5, 182, 182, 182] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 318 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237893 none O=C([O-])C1=CN=C2C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 93, 93, 29, 5, 29, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 93, 93, 5, 1, 1, 1, 1, 1, 201, 201, 201] 201 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, 38]) total number of confs: 396 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: REAL300000237893 none O=C([O-])C1=CN=C2C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 63, 63, 182, 182, 182, 182, 182, 201, 201, 182, 201, 201, 1, 1, 1, 1, 1, 11, 11, 182, 201, 201, 182, 201, 201, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 25, 23, 24, 36, 26, 27, 37] set([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: 405 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237893 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237893 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237893/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237893 Building REAL300000237894 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237894' /scratch/stefan/7769818/working/building/REAL300000237894 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237894 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237894/0 /scratch/stefan/7769818/working/building/REAL300000237894 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/894 `/scratch/stefan/7769818/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1) `REAL300000237894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237894 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 59, 59, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 155, 155, 155, 155, 155, 155, 155, 59, 59, 1, 5, 5, 1, 5, 5] 194 rigid atoms, others: [38, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 282 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237894 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 194, 194, 194, 194, 194, 194, 194, 194, 194, 194, 88, 88, 23, 5, 23, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 194, 194, 194, 88, 88, 5, 1, 1, 1, 1, 1] 194 rigid atoms, others: [39, 40, 41, 42, 43, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 365 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: REAL300000237894 none CC1=C(C(=O)[O-])C2=CC=CC=C2N=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 51, 51, 155, 155, 155, 155, 155, 194, 194, 155, 194, 194, 2, 2, 2, 1, 1, 1, 1, 9, 9, 155, 194, 194, 155, 194, 194] 194 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 34, 35] set([4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 466 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237894 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237894 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237894/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237894 Building REAL300000237895 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237895' /scratch/stefan/7769818/working/building/REAL300000237895 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237895 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237895/0 /scratch/stefan/7769818/working/building/REAL300000237895 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/895 `/scratch/stefan/7769818/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN2C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)=CN=C2C=C1) `REAL300000237895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237895 none O=C([O-])C1=CN2C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 181, 181, 181, 181, 181, 48, 48, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 181, 181, 181, 181, 181, 181, 48, 48, 1, 5, 5, 1, 5, 5, 181, 181, 181] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 291 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237895 none O=C([O-])C1=CN2C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 61, 21, 5, 21, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 61, 61, 5, 1, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 326 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: REAL300000237895 none O=C([O-])C1=CN2C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 55, 55, 181, 181, 181, 181, 181, 201, 201, 181, 201, 201, 1, 1, 1, 1, 1, 1, 11, 11, 181, 201, 201, 181, 201, 201, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 25, 22, 23, 24, 36, 26, 27, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237895 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237895 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237895/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237895 Building REAL300000237896 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237896' /scratch/stefan/7769818/working/building/REAL300000237896 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237896 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237896/0 /scratch/stefan/7769818/working/building/REAL300000237896 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/896 `/scratch/stefan/7769818/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)C=C2)C=N1) `REAL300000237896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237896 none O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 192, 165, 201, 201, 94, 94, 23, 5, 23, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 94, 94, 5, 1, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 591 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237896 none O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 42, 42, 158, 158, 158, 158, 158, 201, 201, 193, 201, 201, 1, 1, 4, 4, 4, 1, 1, 5, 5, 158, 201, 201, 193, 201, 201, 1, 1, 4] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 40, 41, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 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, 42]) total number of confs: 355 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237896 none O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 177, 177, 138, 114, 158, 158, 64, 64, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 158, 158, 177, 177, 177, 158, 158, 64, 64, 1, 5, 5, 1, 5, 5, 158, 158, 177] 201 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 559 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: REAL300000237896 none O=C([O-])C1=CN(C2=CC=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 9, 9, 65, 65, 177, 177, 177, 177, 177, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 4, 4, 9, 9, 177, 201, 201, 201, 201, 201, 4, 4, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 362 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237896 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237896 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237896/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237896 Building REAL300000237897 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237897' /scratch/stefan/7769818/working/building/REAL300000237897 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237897 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237897/0 /scratch/stefan/7769818/working/building/REAL300000237897 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/897 `/scratch/stefan/7769818/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1F) `REAL300000237897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237897 none O=C([O-])C1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 183, 193, 183, 183, 183, 183, 45, 45, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 183, 183, 183, 183, 183, 45, 45, 1, 5, 5, 1, 5, 5] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 334 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237897 none O=C([O-])C1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 64, 64, 27, 5, 27, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 64, 64, 5, 1, 1, 1, 1, 1] 201 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]) total number of confs: 343 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: REAL300000237897 none O=C([O-])C1=CC=CC(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 54, 54, 183, 183, 183, 183, 183, 201, 201, 183, 201, 201, 1, 1, 1, 1, 1, 11, 11, 183, 201, 201, 183, 201, 201] 201 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]) total number of confs: 397 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237897 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237897 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237897/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237897 Building REAL300000237898 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237898' /scratch/stefan/7769818/working/building/REAL300000237898 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237898 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237898/0 /scratch/stefan/7769818/working/building/REAL300000237898 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/898 `/scratch/stefan/7769818/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1Cl) `REAL300000237898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237898 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 150, 63, 53, 63, 63, 24, 24, 11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 63, 63, 63, 201, 201, 63, 63, 24, 24, 1, 5, 5, 3, 5, 5, 63] 201 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 541 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237898 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 153, 66, 55, 66, 66, 27, 27, 14, 5, 14, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 201, 201, 66, 66, 27, 27, 5, 1, 1, 1, 1, 1, 66] 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]) total number of confs: 529 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: REAL300000237898 none O=C([O-])COC1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 33, 7, 1, 1, 1, 1, 1, 1, 5, 5, 19, 19, 63, 63, 63, 63, 63, 66, 66, 63, 66, 66, 1, 1, 1, 25, 25, 1, 1, 5, 5, 63, 66, 66, 66, 66, 66, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 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]) total number of confs: 233 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237898 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237898 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237898/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237898 Building REAL300000237899 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237899' /scratch/stefan/7769818/working/building/REAL300000237899 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237899 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237899/0 /scratch/stefan/7769818/working/building/REAL300000237899 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/899 `/scratch/stefan/7769818/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC=C1C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1) `REAL300000237899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237899 none O=C([O-])C1=CC=CC=C1C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 146, 201, 201, 165, 119, 165, 165, 80, 80, 25, 5, 25, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 165, 165, 201, 201, 201, 201, 165, 165, 80, 80, 5, 1, 1, 1, 1, 1, 165, 165] 201 rigid atoms, others: [39, 40, 41, 42, 43, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45]) total number of confs: 771 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237899 none O=C([O-])C1=CC=CC=C1C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 5, 4, 4, 3, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 34, 34, 131, 131, 131, 131, 131, 165, 165, 131, 165, 165, 1, 1, 4, 3, 4, 4, 1, 1, 5, 5, 131, 165, 165, 131, 165, 165, 1, 1] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 44, 45, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 379 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237899 none O=C([O-])C1=CC=CC=C1C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [185, 185, 185, 185, 185, 119, 185, 185, 131, 92, 131, 131, 57, 57, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 131, 131, 185, 179, 185, 185, 131, 131, 57, 57, 1, 5, 5, 1, 5, 5, 131, 131] 201 rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 709 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: REAL300000237899 none O=C([O-])C1=CC=CC=C1C1=CC=C(C=CC(=O)C2=CN=NN2C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 13, 13, 69, 69, 185, 185, 185, 185, 185, 201, 201, 185, 201, 201, 4, 4, 1, 1, 1, 1, 4, 4, 13, 13, 185, 201, 201, 185, 201, 201, 4, 4] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 33, 30, 31] set([0, 2, 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: 416 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237899 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237899 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237899/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237899 Building REAL300000237900 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237900' /scratch/stefan/7769818/working/building/REAL300000237900 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237900 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237900/0 /scratch/stefan/7769818/working/building/REAL300000237900 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/900 `/scratch/stefan/7769818/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CN=NN1C1=CC=CC=C1) `REAL300000237900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237900 none COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CN=NN1C1=CC=CC=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 169, 169, 169, 169, 169, 169, 169, 169, 169, 62, 62, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 174, 174, 174, 169, 169, 169, 62, 62, 1, 5, 5, 1, 5, 5] 201 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 312 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237900 none COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CN=NN1C1=CC=CC=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 93, 29, 5, 29, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 93, 93, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 398 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: REAL300000237900 none COC1=CC(C(=O)[O-])=CC=C1C=CC(=O)C1=CN=NN1C1=CC=CC=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', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 11, 1, 1, 8, 8, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 54, 54, 169, 169, 169, 169, 169, 201, 201, 169, 201, 201, 4, 4, 4, 1, 1, 1, 9, 9, 169, 201, 201, 194, 201, 201] 201 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]) total number of confs: 493 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237900 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237900 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237900/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237900 Building REAL300000237901 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237901' /scratch/stefan/7769818/working/building/REAL300000237901 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237901 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237901/0 /scratch/stefan/7769818/working/building/REAL300000237901 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/901 `/scratch/stefan/7769818/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)C(F)=CC=C2S1) `REAL300000237901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237901 none O=C([O-])C1=CC2=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 171, 171, 171, 169, 55, 55, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 171, 171, 171, 171, 171, 171, 171, 55, 55, 1, 5, 5, 1, 5, 5, 171, 171] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 305 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237901 none O=C([O-])C1=CC2=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 74, 74, 21, 5, 21, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 74, 74, 5, 1, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38]) 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: REAL300000237901 none O=C([O-])C1=CC2=C(C=CC(=O)C3=CN=NN3C3=CC=CC=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 9, 53, 53, 171, 171, 171, 171, 171, 201, 201, 173, 201, 201, 1, 1, 1, 1, 1, 1, 1, 9, 9, 171, 201, 201, 171, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 22, 23, 24, 25, 26, 27, 28, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 421 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237901 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237901 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237901/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237901 Building REAL300000237902 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237902' /scratch/stefan/7769818/working/building/REAL300000237902 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237902 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237902/0 /scratch/stefan/7769818/working/building/REAL300000237902 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/902 `/scratch/stefan/7769818/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2CC3=C(C=CC(OC)=C3F)C2=O)=CC=C1OCC(=O)[O-]) `REAL300000237902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237902 none COC1=CC(C=C2CC3=C(C=CC(OC)=C3F)C2=O)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 15, 1, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 7, 7, 7, 7, 50, 164, 180, 180, 17, 17, 17, 7, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 164, 164] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 608 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237902 none COC1=CC(C=C2CC3=C(C=CC(OC)=C3F)C2=O)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 15, 1, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 19, 7, 7, 7, 7, 1, 1, 1, 1, 9, 54, 91, 91, 3, 3, 3, 1, 7, 7, 7, 7, 7, 19, 19, 19, 1, 1, 54, 54] 201 rigid atoms, others: [1, 2, 3, 4, 5, 39, 40, 19, 20, 21, 22, 30] set([0, 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, 41, 42]) total number of confs: 336 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237902 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237902 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237902/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237902 Building REAL300000237903 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237903' /scratch/stefan/7769818/working/building/REAL300000237903 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237903 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237903/0 /scratch/stefan/7769818/working/building/REAL300000237903 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/903 `/scratch/stefan/7769818/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])C=C3)CC2=C1F) `REAL300000237903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237903 none COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4] 4 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 9 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237903 none COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 4, 4, 4, 4, 1, 1] 4 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 33, 19, 20, 21, 22, 26, 27, 28] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 29, 30, 31]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237903 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237903 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237903/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237903 Building REAL300000237904 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237904' /scratch/stefan/7769818/working/building/REAL300000237904 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237904 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237904/0 /scratch/stefan/7769818/working/building/REAL300000237904 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/904 `/scratch/stefan/7769818/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(OCC(=O)[O-])C=C3)CC2=C1F) `REAL300000237904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237904 none COC1=CC=C2C(=O)C(=CC3=CC=C(OCC(=O)[O-])C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.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, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 6, 25, 34, 34, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 4, 4, 1, 1, 25, 25, 1, 1, 4, 4] 46 rigid atoms, others: [32, 35, 36, 9, 10, 11, 12, 13, 14, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38]) total number of confs: 127 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237904 none COC1=CC=C2C(=O)C(=CC3=CC=C(OCC(=O)[O-])C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.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, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 3, 4, 15, 46, 46, 46, 4, 4, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 4, 4, 46, 46, 4, 4, 1, 1] 46 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 38, 28, 29, 30, 37] set([0, 32, 34, 35, 36, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 31]) total number of confs: 150 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237904 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237904 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237904/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237904 Building REAL300000237905 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237905' /scratch/stefan/7769818/working/building/REAL300000237905 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237905 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237905/0 /scratch/stefan/7769818/working/building/REAL300000237905 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/905 `/scratch/stefan/7769818/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(OCCC(=O)[O-])C=C3)CC2=C1F) `REAL300000237905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237905 none COC1=CC=C2C(=O)C(=CC3=CC=C(OCCC(=O)[O-])C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 6, 27, 38, 55, 47, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 4, 4, 1, 1, 27, 27, 38, 38, 1, 1, 4, 4] 78 rigid atoms, others: [32, 33, 38, 39, 9, 10, 11, 12, 13, 14, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 40, 41]) total number of confs: 215 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237905 none COC1=CC=C2C(=O)C(=CC3=CC=C(OCCC(=O)[O-])C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 3, 4, 16, 49, 64, 78, 71, 4, 4, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 4, 4, 49, 49, 64, 64, 4, 4, 1, 1] 78 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 40, 41, 22, 23, 24, 25, 29, 30, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 298 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237905 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237905 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237905/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237905 Building REAL300000237906 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237906' /scratch/stefan/7769818/working/building/REAL300000237906 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237906 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237906/0 /scratch/stefan/7769818/working/building/REAL300000237906 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/906 `/scratch/stefan/7769818/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=CC(OC(C)C(=O)[O-])=C3)CC2=C1F) `REAL300000237906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237906 none COC1=CC=C2C(=O)C(=CC3=CC=CC(OC(C)C(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 12, 40, 40, 59, 59, 1, 7, 7, 7, 7, 18, 18, 18, 7, 7, 7, 1, 1, 1, 40, 40, 40, 40, 1, 7, 7] 164 rigid atoms, others: [32, 33, 34, 39, 9, 10, 11, 12, 13, 14, 15, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 40, 41]) total number of confs: 234 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237906 none COC1=CC=C2C(=O)C(=CC3=CC=CC(OC(C)C(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 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, 7, 7, 55, 125, 125, 164, 164, 7, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 7, 7, 125, 125, 125, 125, 7, 1, 1] 164 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 40, 41, 22, 23, 24, 25, 29, 30, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 564 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237906 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237906 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237906/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237906 Building REAL300000237907 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237907' /scratch/stefan/7769818/working/building/REAL300000237907 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237907 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237907/0 /scratch/stefan/7769818/working/building/REAL300000237907 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/907 `/scratch/stefan/7769818/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=CC(OCCC(=O)[O-])=C3)CC2=C1F) `REAL300000237907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237907 none COC1=CC=C2C(=O)C(=CC3=CC=CC(OCCC(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 11, 21, 30, 30, 1, 6, 6, 6, 6, 15, 15, 15, 6, 6, 6, 1, 1, 1, 11, 11, 21, 21, 1, 6, 6] 70 rigid atoms, others: [32, 33, 34, 39, 9, 10, 11, 12, 13, 14, 15, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 40, 41]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237907 none COC1=CC=C2C(=O)C(=CC3=CC=CC(OCCC(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 6, 6, 6, 6, 6, 21, 36, 64, 70, 70, 6, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 6, 6, 6, 36, 36, 64, 64, 6, 1, 1] 70 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 40, 41, 22, 23, 24, 25, 29, 30, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237907 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237907 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237907/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237907 Building REAL300000237908 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237908' /scratch/stefan/7769818/working/building/REAL300000237908 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237908 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237908/0 /scratch/stefan/7769818/working/building/REAL300000237908 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/908 `/scratch/stefan/7769818/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)O3)CC2=C1F) `REAL300000237908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237908 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)O3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.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', '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, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 7, 6, 7, 7, 1, 8, 8, 8, 8, 15, 15, 15, 8, 8, 8, 1, 1, 7, 7, 7, 7, 8, 8] 24 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237908 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)O3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.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', '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, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 7, 7, 1, 1, 1, 1, 24, 24] 24 rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 58 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: REAL300000237908 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)O3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.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', '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, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 24, 24, 8, 8, 24, 24, 24, 24, 8, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 8, 8, 24, 24, 24, 24, 1, 1] 24 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 40, 41, 24, 25, 26, 27, 31] set([0, 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: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237908 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237908 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237908/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237908 Building REAL300000237909 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237909' /scratch/stefan/7769818/working/building/REAL300000237909 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237909 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237909/0 /scratch/stefan/7769818/working/building/REAL300000237909 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/909 `/scratch/stefan/7769818/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=CC(OCC(=O)[O-])=C3)CC2=C1F) `REAL300000237909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237909 none COC1=CC=C2C(=O)C(=CC3=CC=CC(OCC(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.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, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 33, 51, 51, 1, 7, 7, 7, 7, 19, 19, 19, 7, 7, 7, 1, 1, 1, 33, 33, 1, 7, 7] 124 rigid atoms, others: [32, 33, 36, 9, 10, 11, 12, 13, 14, 15, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 37, 38]) total number of confs: 197 number of broken/clashed sets: 44 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237909 none COC1=CC=C2C(=O)C(=CC3=CC=CC(OCC(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.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, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 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, 7, 7, 31, 118, 124, 124, 7, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 7, 7, 118, 118, 7, 1, 1] 124 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 38, 28, 29, 30, 37] set([0, 32, 34, 35, 36, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 31]) total number of confs: 399 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237909 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237909 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237909/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237909 Building REAL300000237910 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237910' /scratch/stefan/7769818/working/building/REAL300000237910 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237910 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237910/0 /scratch/stefan/7769818/working/building/REAL300000237910 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/910 `/scratch/stefan/7769818/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(OC(F)(F)C(=O)[O-])C=C3)CC2=C1F) `REAL300000237910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237910 none COC1=CC=C2C(=O)C(=CC3=CC=C(OC(F)(F)C(=O)[O-])C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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] 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: [10, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 12, 55, 55, 55, 80, 80, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 4, 4, 1, 1, 1, 1, 4, 4] 103 rigid atoms, others: [33, 34, 35, 36, 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, 37, 38]) total number of confs: 287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237910 none COC1=CC=C2C(=O)C(=CC3=CC=C(OC(F)(F)C(=O)[O-])C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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] 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 2, 27, 87, 86, 86, 103, 103, 4, 4, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 4, 4, 4, 4, 1, 1] 103 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 38, 37, 30, 31] set([0, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237910 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237910 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237910/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237910 Building REAL300000237911 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237911' /scratch/stefan/7769818/working/building/REAL300000237911 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237911 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237911/0 /scratch/stefan/7769818/working/building/REAL300000237911 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/911 `/scratch/stefan/7769818/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=C4C=C(C(=O)[O-])OC4=C(OC)C=C3)CC2=C1F) `REAL300000237911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237911 none COC1=CC=C2C(=O)C(=CC3=C4C=C(C(=O)[O-])OC4=C(OC)C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 12, 5, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 6, 6, 1, 3, 3, 3, 1, 1, 6, 6] 11 rigid atoms, others: [34, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 40, 41]) total number of confs: 26 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237911 none COC1=CC=C2C(=O)C(=CC3=C4C=C(C(=O)[O-])OC4=C(OC)C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 12, 5, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 6, 6, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 6, 11, 11, 11, 6, 6, 1, 1] 11 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 40, 41, 24, 25, 26, 27, 31] set([0, 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: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237911 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237911 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237911/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237911 Building REAL300000237912 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237912' /scratch/stefan/7769818/working/building/REAL300000237912 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237912 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237912/0 /scratch/stefan/7769818/working/building/REAL300000237912 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/912 `/scratch/stefan/7769818/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CN(CC(=O)[O-])N=N3)CC2=C1F) `REAL300000237912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237912 none COC1=CC=C2C(=O)C(=CC3=CN(CC(=O)[O-])N=N3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 8, 13, 13, 1, 1, 8, 8, 8, 8, 19, 19, 19, 8, 8, 8, 1, 8, 8, 8, 8] 35 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237912 none COC1=CC=C2C(=O)C(=CC3=CN(CC(=O)[O-])N=N3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 34, 35, 35, 8, 8, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 8, 34, 34, 1, 1] 35 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 19, 20, 21, 22, 26, 27, 28] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 29, 30, 31]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237912 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237912 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237912/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237912 Building REAL300000237913 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237913' /scratch/stefan/7769818/working/building/REAL300000237913 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237913 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237913/0 /scratch/stefan/7769818/working/building/REAL300000237913 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/913 `/scratch/stefan/7769818/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=CC(C(=O)[O-])=C3)CC2=C1F) `REAL300000237913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237913 none COC1=CC=C2C(=O)C(=CC3=CC=CC(C(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7] 7 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237913 none COC1=CC=C2C(=O)C(=CC3=CC=CC(C(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 33, 19, 20, 21, 22, 26, 27, 28] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 29, 30, 31]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237913 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237913 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237913/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237913 Building REAL300000237914 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237914' /scratch/stefan/7769818/working/building/REAL300000237914 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237914 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237914/0 /scratch/stefan/7769818/working/building/REAL300000237914 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/914 `/scratch/stefan/7769818/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=CS3)CC2=C1F) `REAL300000237914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237914 none COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=CS3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 7, 7] 7 rigid atoms, others: [9, 10, 11, 12, 13, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237914 none COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=CS3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 1, 1] 7 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 25, 26, 27, 30, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 28, 29]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237914 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237914 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237914/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237914 Building REAL300000237915 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237915' /scratch/stefan/7769818/working/building/REAL300000237915 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237915 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237915/0 /scratch/stefan/7769818/working/building/REAL300000237915 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/915 `/scratch/stefan/7769818/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2CC3=C(C=CC(OC)=C3F)C2=O)=CC=C1OCCC(=O)[O-]) `REAL300000237915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237915 none COC1=CC(C=C2CC3=C(C=CC(OC)=C3F)C2=O)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 15, 1, 11, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 5, 5, 5, 5, 35, 108, 145, 163, 163, 13, 13, 13, 5, 1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 108, 108, 145, 145] 180 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 36] set([0, 1, 2, 3, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 649 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237915 none COC1=CC(C=C2CC3=C(C=CC(OC)=C3F)C2=O)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 15, 1, 11, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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 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, 5, 5, 5, 5, 5, 13, 5, 5, 5, 5, 1, 1, 1, 1, 9, 40, 59, 87, 87, 4, 4, 4, 1, 5, 5, 5, 5, 5, 13, 13, 13, 1, 1, 40, 40, 59, 59] 180 rigid atoms, others: [1, 2, 3, 4, 5, 40, 41, 19, 20, 21, 22, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 377 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237915 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237915 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237915/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237915 Building REAL300000237916 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237916' /scratch/stefan/7769818/working/building/REAL300000237916 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237916 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237916/0 /scratch/stefan/7769818/working/building/REAL300000237916 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/916 `/scratch/stefan/7769818/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])C=C3Cl)CC2=C1F) `REAL300000237916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237916 none COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])C=C3Cl)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 6, 6] 6 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237916 none COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])C=C3Cl)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 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, 1, 1, 1, 1, 6, 6, 1, 2, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 6, 6, 6, 1, 1] 6 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 20, 21, 22, 23, 33, 27, 28, 29] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 30, 31]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237916 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237916 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237916/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237916 Building REAL300000237917 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237917' /scratch/stefan/7769818/working/building/REAL300000237917 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237917 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237917/0 /scratch/stefan/7769818/working/building/REAL300000237917 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/917 `/scratch/stefan/7769818/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=CC(C(=O)[O-])=C3Cl)CC2=C1F) `REAL300000237917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237917 none COC1=CC=C2C(=O)C(=CC3=CC=CC(C(=O)[O-])=C3Cl)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 6, 6, 1, 1, 1, 6, 6] 10 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237917 none COC1=CC=C2C(=O)C(=CC3=CC=CC(C(=O)[O-])=C3Cl)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 6, 6, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 6, 6, 6, 1, 1] 10 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 20, 21, 22, 23, 33, 27, 28, 29] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 30, 31]) total number of confs: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237917 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237917 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237917/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237917 Building REAL300000237918 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237918' /scratch/stefan/7769818/working/building/REAL300000237918 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237918 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237918/0 /scratch/stefan/7769818/working/building/REAL300000237918 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/918 `/scratch/stefan/7769818/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(O)C(C(=O)[O-])=C3)CC2=C1F) `REAL300000237918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237918 none COC1=CC=C2C(=O)C(=CC3=CC=C(O)C(C(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 2, 1, 7, 7] 14 rigid atoms, others: [33, 9, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 34, 35]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237918 none COC1=CC=C2C(=O)C(=CC3=CC=C(O)C(C(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 14, 7, 1, 1] 14 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 20, 21, 22, 23, 27, 28, 29] set([0, 32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 30, 31]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237918 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237918 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237918/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237918 Building REAL300000237919 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237919' /scratch/stefan/7769818/working/building/REAL300000237919 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237919 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237919/0 /scratch/stefan/7769818/working/building/REAL300000237919 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/919 `/scratch/stefan/7769818/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=C(C)C=C3C)CC2=C1F) `REAL300000237919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237919 none COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=C(C)C=C3C)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 6, 6, 1, 2, 2, 2, 1, 2, 2, 2, 6, 6] 11 rigid atoms, others: [35, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237919 none COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=C(C)C=C3C)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 11 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 40, 21, 22, 23, 24, 28, 29, 30] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237919 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237919 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237919/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237919 Building REAL300000237920 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237920' /scratch/stefan/7769818/working/building/REAL300000237920 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237920 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237920/0 /scratch/stefan/7769818/working/building/REAL300000237920 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/920 `/scratch/stefan/7769818/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(OC(C)C(=O)[O-])C=C3)CC2=C1F) `REAL300000237920.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237920 none COC1=CC=C2C(=O)C(=CC3=CC=C(OC(C)C(=O)[O-])C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 13, 39, 39, 49, 49, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 4, 4, 1, 1, 39, 39, 39, 39, 1, 1, 4, 4] 61 rigid atoms, others: [32, 33, 38, 39, 9, 10, 11, 12, 13, 14, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 40, 41]) total number of confs: 182 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237920 none COC1=CC=C2C(=O)C(=CC3=CC=C(OC(C)C(=O)[O-])C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 3, 4, 27, 53, 53, 61, 61, 4, 4, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 4, 4, 53, 53, 53, 53, 4, 4, 1, 1] 61 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 40, 41, 22, 23, 24, 25, 29, 30, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 200 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237920 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237920 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237920/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237920 Building REAL300000237921 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237921' /scratch/stefan/7769818/working/building/REAL300000237921 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237921 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237921/0 /scratch/stefan/7769818/working/building/REAL300000237921 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/921 `/scratch/stefan/7769818/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=CC=C3OCCC(=O)[O-])CC2=C1F) `REAL300000237921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237921 none COC1=CC=C2C(=O)C(=CC3=CC=CC=C3OCCC(=O)[O-])CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 42, 73, 97, 93, 6, 6, 6, 6, 16, 16, 16, 6, 6, 6, 1, 1, 1, 1, 42, 42, 73, 73, 6, 6] 179 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41]) total number of confs: 398 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237921 none COC1=CC=C2C(=O)C(=CC3=CC=CC=C3OCCC(=O)[O-])CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 6, 6, 2, 6, 6, 6, 38, 116, 160, 179, 172, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 6, 6, 6, 6, 116, 116, 160, 160, 1, 1] 179 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 40, 41, 22, 23, 24, 25, 29, 30, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 683 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237921 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237921 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237921/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237921 Building REAL300000237922 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237922' /scratch/stefan/7769818/working/building/REAL300000237922 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237922 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237922/0 /scratch/stefan/7769818/working/building/REAL300000237922 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/922 `/scratch/stefan/7769818/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=C(C(=O)[O-])C=NN3C)CC2=C1F) `REAL300000237922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237922 none COC1=CC=C2C(=O)C(=CC3=C(C(=O)[O-])C=NN3C)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 7, 9, 9, 9, 7, 7, 7, 1, 2, 2, 2, 7, 7] 9 rigid atoms, others: [9, 10, 11, 12, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237922 none COC1=CC=C2C(=O)C(=CC3=C(C(=O)[O-])C=NN3C)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 8, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 7, 7, 1, 1] 9 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 33, 19, 20, 21, 22, 26, 27, 28] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 29, 30, 31]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237922 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237922 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237922/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237922 Building REAL300000237923 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237923' /scratch/stefan/7769818/working/building/REAL300000237923 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237923 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237923/0 /scratch/stefan/7769818/working/building/REAL300000237923 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/923 `/scratch/stefan/7769818/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])C(F)=C3)CC2=C1F) `REAL300000237923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237923 none COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])C(F)=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 7, 7, 7, 7, 9, 9, 9, 7, 7, 7, 1, 1, 1, 7, 7] 9 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237923 none COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])C(F)=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 9, 9, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 7, 7, 1, 1] 9 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 20, 21, 22, 23, 33, 27, 28, 29] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 30, 31]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237923 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237923 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237923/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237923 Building REAL300000237924 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237924' /scratch/stefan/7769818/working/building/REAL300000237924 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237924 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237924/0 /scratch/stefan/7769818/working/building/REAL300000237924 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/924 `/scratch/stefan/7769818/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(C=CC(=O)[O-])O3)CC2=C1F) `REAL300000237924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237924 none COC1=CC=C2C(=O)C(=CC3=CC=C(C=CC(=O)[O-])O3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [21, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 12, 12, 23, 23, 1, 8, 8, 8, 8, 21, 21, 21, 8, 8, 8, 1, 1, 12, 12, 8, 8] 42 rigid atoms, others: [9, 10, 11, 12, 13, 14, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237924 none COC1=CC=C2C(=O)C(=CC3=CC=C(C=CC(=O)[O-])O3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 31, 31, 42, 42, 8, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 8, 8, 31, 31, 1, 1] 42 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 20, 21, 22, 23, 27, 28, 29] set([0, 32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 30, 31]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237924 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237924 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237924/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237924 Building REAL300000237925 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237925' /scratch/stefan/7769818/working/building/REAL300000237925 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237925 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237925/0 /scratch/stefan/7769818/working/building/REAL300000237925 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/925 `/scratch/stefan/7769818/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=C2CC3=C(C=CC(OC)=C3F)C2=O)C=C1C(=O)[O-]) `REAL300000237925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237925 none COC1=CC=C(C=C2CC3=C(C=CC(OC)=C3F)C2=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.2', '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, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 15, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 3, 3, 3, 7] 25 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 37, 38, 15, 35, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237925 none COC1=CC=C(C=C2CC3=C(C=CC(OC)=C3F)C2=O)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.2', '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, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 15, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 13, 7, 7, 7, 7, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 7, 7, 7, 7, 7, 13, 13, 13, 1] 25 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 38, 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237925 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237925 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237925/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237925 Building REAL300000237926 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237926' /scratch/stefan/7769818/working/building/REAL300000237926 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237926 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237926/0 /scratch/stefan/7769818/working/building/REAL300000237926 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/926 `/scratch/stefan/7769818/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=CC=C3F)CC2=C1F) `REAL300000237926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237926 none COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=CC=C3F)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7] 7 rigid atoms, others: [32, 9, 10, 11, 12, 13, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237926 none COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=CC=C3F)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 7, 1, 1] 7 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 20, 21, 22, 23, 33, 27, 28, 29] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 30, 31]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237926 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237926 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237926/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237926 Building REAL300000237927 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237927' /scratch/stefan/7769818/working/building/REAL300000237927 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237927 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237927/0 /scratch/stefan/7769818/working/building/REAL300000237927 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/927 `/scratch/stefan/7769818/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C(=O)[O-])C=C1C=C1CC2=C(C=CC(OC)=C2F)C1=O) `REAL300000237927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237927 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=C1CC2=C(C=CC(OC)=C2F)C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 15, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 7, 7, 7, 7, 15, 7, 7, 12, 12, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 16, 16, 16, 7, 15, 15, 15, 7, 1, 1, 1, 1, 1, 3, 3, 3] 43 rigid atoms, others: [35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237927 none COC1=CC(OC)=C(C(=O)[O-])C=C1C=C1CC2=C(C=CC(OC)=C2F)C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 15, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 1, 1, 3, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 15, 7, 7, 7, 7, 4, 4, 4, 1, 4, 4, 4, 1, 7, 7, 7, 7, 7, 15, 15, 15] 43 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 11, 12, 34, 13, 30] set([0, 6, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237927 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237927 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237927/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237927 Building REAL300000237928 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237928' /scratch/stefan/7769818/working/building/REAL300000237928 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237928 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237928/0 /scratch/stefan/7769818/working/building/REAL300000237928 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/928 `/scratch/stefan/7769818/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(F)C(C(=O)[O-])=C3)CC2=C1F) `REAL300000237928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237928 none COC1=CC=C2C(=O)C(=CC3=CC=C(F)C(C(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 7, 7, 7, 7, 13, 13, 13, 7, 7, 7, 1, 1, 1, 7, 7] 13 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237928 none COC1=CC=C2C(=O)C(=CC3=CC=C(F)C(C(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 13, 13, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 7, 1, 1] 13 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 20, 21, 22, 23, 33, 27, 28, 29] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 30, 31]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237928 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237928 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237928/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237928 Building REAL300000237929 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237929' /scratch/stefan/7769818/working/building/REAL300000237929 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237929 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237929/0 /scratch/stefan/7769818/working/building/REAL300000237929 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/929 `/scratch/stefan/7769818/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(CC(=O)[O-])C=C3)CC2=C1F) `REAL300000237929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237929 none COC1=CC=C2C(=O)C(=CC3=CC=C(CC(=O)[O-])C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 4, 4, 1, 1, 2, 2, 1, 1, 4, 4] 7 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: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237929 none COC1=CC=C2C(=O)C(=CC3=CC=C(CC(=O)[O-])C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 3, 6, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 4, 4, 6, 6, 4, 4, 1, 1] 7 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 36, 27, 28, 29, 37] set([0, 32, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 30, 31]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237929 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237929 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237929/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237929 Building REAL300000237930 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237930' /scratch/stefan/7769818/working/building/REAL300000237930 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237930 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237930/0 /scratch/stefan/7769818/working/building/REAL300000237930 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/930 `/scratch/stefan/7769818/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC(Br)=CC(C(=O)[O-])=C3)CC2=C1F) `REAL300000237930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237930 none COC1=CC=C2C(=O)C(=CC3=CC(Br)=CC(C(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7] 7 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237930 none COC1=CC=C2C(=O)C(=CC3=CC(Br)=CC(C(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 7, 1, 1] 7 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 20, 21, 22, 23, 33, 27, 28, 29] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 30, 31]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237930 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237930 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237930/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237930 Building REAL300000237931 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237931' /scratch/stefan/7769818/working/building/REAL300000237931 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237931 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237931/0 /scratch/stefan/7769818/working/building/REAL300000237931 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/931 `/scratch/stefan/7769818/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])S3)CC2=C1F) `REAL300000237931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237931 none COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])S3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 7, 7] 7 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237931 none COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])S3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 1, 1] 7 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 25, 26, 27, 30, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 28, 29]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237931 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237931 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237931/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237931 Building REAL300000237932 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237932' /scratch/stefan/7769818/working/building/REAL300000237932 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237932 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237932/0 /scratch/stefan/7769818/working/building/REAL300000237932 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/932 `/scratch/stefan/7769818/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(C=CC(=O)[O-])C=C3)CC2=C1F) `REAL300000237932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237932 none COC1=CC=C2C(=O)C(=CC3=CC=C(C=CC(=O)[O-])C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.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, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 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, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 1, 1, 4, 4, 4, 4, 9, 9, 9, 4, 4, 4, 1, 1, 5, 5, 1, 1, 4, 4] 13 rigid atoms, others: [32, 35, 36, 9, 10, 11, 12, 13, 14, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38]) total number of confs: 43 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237932 none COC1=CC=C2C(=O)C(=CC3=CC=C(C=CC(=O)[O-])C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.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, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 3, 9, 9, 13, 13, 4, 4, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 4, 4, 9, 9, 4, 4, 1, 1] 13 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 38, 28, 29, 30, 37] set([0, 32, 34, 35, 36, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 31]) total number of confs: 48 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237932 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237932 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237932/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237932 Building REAL300000237933 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237933' /scratch/stefan/7769818/working/building/REAL300000237933 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237933 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237933/0 /scratch/stefan/7769818/working/building/REAL300000237933 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/933 `/scratch/stefan/7769818/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC(F)=C(C(=O)[O-])C=C3F)CC2=C1F) `REAL300000237933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237933 none COC1=CC=C2C(=O)C(=CC3=CC(F)=C(C(=O)[O-])C=C3F)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 7, 7, 7, 7, 9, 9, 9, 7, 7, 7, 1, 1, 7, 7] 9 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237933 none COC1=CC=C2C(=O)C(=CC3=CC(F)=C(C(=O)[O-])C=C3F)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 9, 9, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 7, 1, 1] 9 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 21, 22, 23, 24, 33, 28, 29, 30] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 31]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237933 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237933 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237933/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237933 Building REAL300000237934 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237934' /scratch/stefan/7769818/working/building/REAL300000237934 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237934 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237934/0 /scratch/stefan/7769818/working/building/REAL300000237934 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/934 `/scratch/stefan/7769818/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=C4C(=CC=C3)NN=C4C(=O)[O-])CC2=C1F) `REAL300000237934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237934 none COC1=CC=C2C(=O)C(=CC3=C4C(=CC=C3)NN=C4C(=O)[O-])CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 6, 6] 10 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237934 none COC1=CC=C2C(=O)C(=CC3=C4C(=CC=C3)NN=C4C(=O)[O-])CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 6, 6, 6, 6, 1, 1] 10 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 37, 25, 22, 23, 24, 36, 29, 30, 31] set([0, 32, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28]) total number of confs: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237934 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237934 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237934/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237934 Building REAL300000237935 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237935' /scratch/stefan/7769818/working/building/REAL300000237935 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237935 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237935/0 /scratch/stefan/7769818/working/building/REAL300000237935 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/935 `/scratch/stefan/7769818/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CN(CC(=O)[O-])N=C3C3=CC=CC=C3)CC2=C1F) `REAL300000237935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237935 none COC1=CC=C2C(=O)C(=CC3=CN(CC(=O)[O-])N=C3C3=CC=CC=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 8, 13, 13, 1, 1, 1, 7, 7, 1, 7, 7, 7, 7, 7, 7, 16, 16, 16, 7, 7, 7, 1, 8, 8, 7, 7, 1, 7, 7, 7, 7] 59 rigid atoms, others: [35, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237935 none COC1=CC=C2C(=O)C(=CC3=CN(CC(=O)[O-])N=C3C3=CC=CC=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [37, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 25, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 37, 37, 37, 20, 20, 20, 7, 25, 25, 1, 1, 1, 1, 1, 20, 20] 59 rigid atoms, others: [38, 39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44]) 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: REAL300000237935 none COC1=CC=C2C(=O)C(=CC3=CN(CC(=O)[O-])N=C3C3=CC=CC=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 59 conformations in input total number of sets (complete confs): 59 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, 30, 36, 36, 7, 7, 7, 20, 20, 7, 20, 20, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 30, 30, 20, 20, 7, 20, 20, 1, 1] 59 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 9, 10, 7, 44, 34, 43, 25, 26, 27, 28] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237935 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237935 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237935/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237935 Building REAL300000237936 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237936' /scratch/stefan/7769818/working/building/REAL300000237936 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237936 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237936/0 /scratch/stefan/7769818/working/building/REAL300000237936 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/936 `/scratch/stefan/7769818/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C(O)=C4)O3)CC2=C1F) `REAL300000237936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237936 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C(O)=C4)O3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [19, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 22, 22, 12, 12, 12, 1, 8, 8, 8, 8, 19, 19, 19, 8, 8, 8, 1, 1, 12, 12, 24, 12, 8, 8] 152 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237936 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C(O)=C4)O3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [76, 72, 72, 72, 72, 72, 72, 72, 72, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 12, 72, 72, 72, 72, 76, 76, 76, 72, 72, 72, 12, 12, 1, 1, 2, 1, 72, 72] 152 rigid atoms, others: [37, 38, 40, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 41, 42]) 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: REAL300000237936 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C(O)=C4)O3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 72, 72, 72, 72, 76, 76, 72, 72, 72, 8, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 8, 8, 72, 72, 144, 72, 1, 1] 152 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 9, 10, 7, 34, 41, 25, 26, 27, 28, 42] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237936 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237936 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237936/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237936 Building REAL300000237937 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237937' /scratch/stefan/7769818/working/building/REAL300000237937 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237937 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237937/0 /scratch/stefan/7769818/working/building/REAL300000237937 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/937 `/scratch/stefan/7769818/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)C=C3)CC2=C1F) `REAL300000237937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237937 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 2, 2, 3, 3, 3, 3, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 3, 3, 3, 3, 1, 1, 4, 4] 6 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 43, 44]) total number of confs: 19 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237937 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 6, 6] 6 rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44]) total number of confs: 18 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: REAL300000237937 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', '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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 4, 4, 3, 4, 6, 6, 3, 4, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 4, 4, 6, 6, 6, 6, 4, 4, 1, 1] 6 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 9, 10, 7, 44, 34, 43, 25, 26, 27, 28] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 32 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237937 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237937 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237937/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237937 Building REAL300000237938 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237938' /scratch/stefan/7769818/working/building/REAL300000237938 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237938 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237938/0 /scratch/stefan/7769818/working/building/REAL300000237938 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/938 `/scratch/stefan/7769818/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CNC4=CC=C(C(=O)[O-])C=C34)CC2=C1F) `REAL300000237938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237938 none COC1=CC=C2C(=O)C(=CC3=CNC4=CC=C(C(=O)[O-])C=C34)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7] 7 rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237938 none COC1=CC=C2C(=O)C(=CC3=CNC4=CC=C(C(=O)[O-])C=C34)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 37, 22, 23, 24, 25, 38, 29, 30, 31] set([0, 32, 34, 35, 36, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237938 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237938 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237938/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237938 Building REAL300000237939 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237939' /scratch/stefan/7769818/working/building/REAL300000237939 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237939 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237939/0 /scratch/stefan/7769818/working/building/REAL300000237939 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/939 `/scratch/stefan/7769818/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])N=C3)CC2=C1F) `REAL300000237939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237939 none COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])N=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7] 7 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237939 none COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])N=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 7, 1, 1] 7 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 19, 20, 21, 22, 26, 27, 28] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 29, 30, 31]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237939 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237939 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237939/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237939 Building REAL300000237940 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237940' /scratch/stefan/7769818/working/building/REAL300000237940 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237940 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237940/0 /scratch/stefan/7769818/working/building/REAL300000237940 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/940 `/scratch/stefan/7769818/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])C(O)=C3)CC2=C1F) `REAL300000237940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237940 none COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])C(O)=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 1 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: [9, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 7, 7, 7, 7, 9, 9, 9, 7, 7, 7, 1, 1, 2, 1, 7, 7] 18 rigid atoms, others: [33, 9, 10, 11, 12, 13, 14, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 34, 35]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237940 none COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])C(O)=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 9, 9, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 14, 7, 1, 1] 18 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 20, 21, 22, 23, 27, 28, 29] set([0, 32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 30, 31]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237940 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237940 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237940/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237940 Building REAL300000237941 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237941' /scratch/stefan/7769818/working/building/REAL300000237941 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237941 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237941/0 /scratch/stefan/7769818/working/building/REAL300000237941 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/941 `/scratch/stefan/7769818/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(C)C(C(=O)[O-])=C3)CC2=C1F) `REAL300000237941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237941 none COC1=CC=C2C(=O)C(=CC3=CC=C(C)C(C(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', '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, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 2, 2, 2, 1, 7, 7] 7 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 36, 37]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237941 none COC1=CC=C2C(=O)C(=CC3=CC=C(C)C(C(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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', '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, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 36, 27, 28, 29, 37] set([0, 32, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 30, 31]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237941 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237941 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237941/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237941 Building REAL300000237942 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237942' /scratch/stefan/7769818/working/building/REAL300000237942 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237942 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237942/0 /scratch/stefan/7769818/working/building/REAL300000237942 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/942 `/scratch/stefan/7769818/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=C(Cl)S3)CC2=C1F) `REAL300000237942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237942 none COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=C(Cl)S3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 7, 7, 1, 7, 7] 13 rigid atoms, others: [9, 10, 11, 12, 13, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237942 none COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=C(Cl)S3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 14, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 1, 1] 13 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 26, 27, 28, 30, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 29]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237942 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237942 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237942/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237942 Building REAL300000237943 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237943' /scratch/stefan/7769818/working/building/REAL300000237943 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237943 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237943/0 /scratch/stefan/7769818/working/building/REAL300000237943 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/943 `/scratch/stefan/7769818/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=C(C)O3)CC2=C1F) `REAL300000237943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237943 none COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=C(C)O3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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] 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, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 9, 9, 9, 9, 14, 14, 14, 9, 9, 9, 1, 1, 1, 1, 9, 9] 14 rigid atoms, others: [32, 9, 10, 11, 12, 13, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237943 none COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=C(C)O3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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] 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 14, 14, 9, 9, 9, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 9, 9, 9, 9, 1, 1] 14 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 33, 19, 20, 21, 22, 26, 27, 28] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 29, 30, 31]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237943 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237943 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237943/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237943 Building REAL300000237944 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237944' /scratch/stefan/7769818/working/building/REAL300000237944 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237944 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237944/0 /scratch/stefan/7769818/working/building/REAL300000237944 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/944 `/scratch/stefan/7769818/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)S3)CC2=C1F) `REAL300000237944.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237944 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)S3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 1, 2, 6, 6, 6, 6, 1, 7, 7, 7, 7, 13, 13, 13, 7, 7, 7, 1, 1, 6, 6, 6, 6, 7, 7] 18 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237944 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)S3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 1, 1, 1, 1, 18, 18] 18 rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 43 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: REAL300000237944 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(C(=O)[O-])C=C4)S3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 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, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 18, 18, 7, 13, 18, 18, 18, 18, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 18, 18, 18, 18, 1, 1] 18 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 40, 41, 24, 25, 26, 27, 31] set([0, 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: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237944 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237944 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237944/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237944 Building REAL300000237945 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237945' /scratch/stefan/7769818/working/building/REAL300000237945 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237945 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237945/0 /scratch/stefan/7769818/working/building/REAL300000237945 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/945 `/scratch/stefan/7769818/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=NN3C)CC2=C1F) `REAL300000237945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237945 none COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=NN3C)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 2, 2, 2, 6, 6] 6 rigid atoms, others: [9, 10, 11, 12, 13, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237945 none COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=NN3C)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 8, 8, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 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, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 6, 6, 6, 6, 1, 1] 6 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 33, 19, 20, 21, 22, 26, 27, 28] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 29, 30, 31]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237945 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237945 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237945/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237945 Building REAL300000237946 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237946' /scratch/stefan/7769818/working/building/REAL300000237946 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237946 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237946/0 /scratch/stefan/7769818/working/building/REAL300000237946 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/946 `/scratch/stefan/7769818/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(O)C(C(=O)[O-])=C4)O3)CC2=C1F) `REAL300000237946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237946 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(O)C(C(=O)[O-])=C4)O3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [19, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 13, 13, 12, 12, 13, 13, 13, 13, 13, 1, 8, 8, 8, 8, 19, 19, 19, 8, 8, 8, 1, 1, 13, 13, 26, 13, 8, 8] 150 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237946 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(O)C(C(=O)[O-])=C4)O3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [75, 75, 75, 75, 75, 75, 75, 75, 75, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 13, 13, 1, 1, 2, 1, 75, 75] 150 rigid atoms, others: [37, 38, 40, 13, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 41, 42]) total number of confs: 168 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: REAL300000237946 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=C(O)C(C(=O)[O-])=C4)O3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 75, 75, 75, 75, 75, 75, 75, 75, 75, 8, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 8, 8, 75, 75, 150, 75, 1, 1] 150 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 9, 10, 7, 34, 41, 25, 26, 27, 28, 42] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237946 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237946 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237946/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237946 Building REAL300000237947 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237947' /scratch/stefan/7769818/working/building/REAL300000237947 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237947 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237947/0 /scratch/stefan/7769818/working/building/REAL300000237947 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/947 `/scratch/stefan/7769818/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CN=CC(C(=O)[O-])=C3)CC2=C1F) `REAL300000237947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237947 none COC1=CC=C2C(=O)C(=CC3=CN=CC(C(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7] 7 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237947 none COC1=CC=C2C(=O)C(=CC3=CN=CC(C(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 7, 1, 1] 7 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 19, 20, 21, 22, 26, 27, 28] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 29, 30, 31]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237947 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237947 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237947/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237947 Building REAL300000237948 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237948' /scratch/stefan/7769818/working/building/REAL300000237948 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237948 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237948/0 /scratch/stefan/7769818/working/building/REAL300000237948 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/948 `/scratch/stefan/7769818/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=CO3)CC2=C1F) `REAL300000237948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237948 none COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=CO3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 9, 9] 9 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237948 none COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=CO3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 9, 9, 1, 1] 9 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 25, 26, 27, 30, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 28, 29]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237948 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237948 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237948/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237948 Building REAL300000237949 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237949' /scratch/stefan/7769818/working/building/REAL300000237949 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237949 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237949/0 /scratch/stefan/7769818/working/building/REAL300000237949 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/949 `/scratch/stefan/7769818/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=CC(C(=O)[O-])=C4)S3)CC2=C1F) `REAL300000237949.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237949 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=CC(C(=O)[O-])=C4)S3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 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, 7, 7, 7, 7, 3, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 12, 1, 7, 7, 7, 7, 14, 14, 14, 7, 7, 7, 1, 1, 12, 12, 12, 12, 7, 7] 34 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237949 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=CC(C(=O)[O-])=C4)S3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 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, 7, 7, 7, 7, 3, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 12, 1, 1, 1, 1, 34, 34] 34 rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 83 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: REAL300000237949 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=CC(C(=O)[O-])=C4)S3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.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, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 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, 7, 7, 7, 7, 3, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 34, 34, 34, 34, 34, 34, 34, 34, 7, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 7, 34, 34, 34, 34, 1, 1] 34 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 40, 41, 24, 25, 26, 27, 31] set([0, 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: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237949 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237949 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237949/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237949 Building REAL300000237950 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237950' /scratch/stefan/7769818/working/building/REAL300000237950 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237950 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237950/0 /scratch/stefan/7769818/working/building/REAL300000237950 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/950 `/scratch/stefan/7769818/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=C1CC2=C(C=CC(OC)=C2F)C1=O) `REAL300000237950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237950 none COC1=CC=C(C(=O)[O-])C=C1C=C1CC2=C(C=CC(OC)=C2F)C1=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', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.2', 'O.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, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 15, 1, 11, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 3, 3, 3] 13 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 37, 20, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237950 none COC1=CC=C(C(=O)[O-])C=C1C=C1CC2=C(C=CC(OC)=C2F)C1=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', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.2', 'O.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, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 15, 1, 11, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 13, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 7, 7, 7, 7, 7, 13, 13, 13] 13 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]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237950 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237950 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237950/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237950 Building REAL300000237951 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237951' /scratch/stefan/7769818/working/building/REAL300000237951 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237951 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237951/0 /scratch/stefan/7769818/working/building/REAL300000237951 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/951 `/scratch/stefan/7769818/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CSC4=CC=C(C(=O)[O-])C=C34)CC2=C1F) `REAL300000237951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237951 none COC1=CC=C2C(=O)C(=CC3=CSC4=CC=C(C(=O)[O-])C=C34)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6] 6 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 36, 37, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237951 none COC1=CC=C2C(=O)C(=CC3=CSC4=CC=C(C(=O)[O-])C=C34)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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] 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, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 6, 6, 6, 6, 1, 1] 6 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 37, 25, 22, 23, 24, 36, 29, 30, 31] set([0, 32, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237951 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237951 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237951/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237951 Building REAL300000237952 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237952' /scratch/stefan/7769818/working/building/REAL300000237952 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237952 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237952/0 /scratch/stefan/7769818/working/building/REAL300000237952 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/952 `/scratch/stefan/7769818/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=CC=C3Br)CC2=C1F) `REAL300000237952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237952 none COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=CC=C3Br)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 6, 6] 6 rigid atoms, others: [32, 9, 10, 11, 12, 13, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237952 none COC1=CC=C2C(=O)C(=CC3=CC(C(=O)[O-])=CC=C3Br)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 6, 6, 6, 1, 1] 6 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 20, 21, 22, 23, 33, 27, 28, 29] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 30, 31]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237952 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237952 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237952/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237952 Building REAL300000237953 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237953' /scratch/stefan/7769818/working/building/REAL300000237953 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237953 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237953/0 /scratch/stefan/7769818/working/building/REAL300000237953 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/953 `/scratch/stefan/7769818/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])C=C3[N+](=O)[O-])CC2=C1F) `REAL300000237953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237953 none COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])C=C3[N+](=O)[O-])CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5] 5 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237953 none COC1=CC=C2C(=O)C(=CC3=CC=C(C(=O)[O-])C=C3[N+](=O)[O-])CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 2, 4, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 5, 5, 5, 1, 1] 5 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 35, 25, 22, 23, 24, 36, 29, 30, 31] set([0, 32, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237953 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237953 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237953/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237953 Building REAL300000237954 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237954' /scratch/stefan/7769818/working/building/REAL300000237954 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237954 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237954/0 /scratch/stefan/7769818/working/building/REAL300000237954 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/954 `/scratch/stefan/7769818/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=CC(CC(=O)[O-])=C3)CC2=C1F) `REAL300000237954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237954 none COC1=CC=C2C(=O)C(=CC3=CC=CC(CC(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 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: [14, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 7, 7, 7, 7, 14, 14, 14, 7, 7, 7, 1, 1, 1, 2, 2, 1, 7, 7] 19 rigid atoms, others: [32, 35, 9, 10, 11, 12, 13, 14, 15, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 36, 37]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237954 none COC1=CC=C2C(=O)C(=CC3=CC=CC(CC(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 12, 19, 19, 7, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 7, 2, 12, 12, 7, 1, 1] 19 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 36, 27, 28, 29, 37] set([0, 32, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 30, 31]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237954 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237954 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237954/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237954 Building REAL300000237955 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237955' /scratch/stefan/7769818/working/building/REAL300000237955 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237955 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237955/0 /scratch/stefan/7769818/working/building/REAL300000237955 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/955 `/scratch/stefan/7769818/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=C2CC3=C(C=CC(OC)=C3F)C2=O)=CC=C1C(=O)[O-]) `REAL300000237955.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237955 none COC1=CC(C=C2CC3=C(C=CC(OC)=C3F)C2=O)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 15, 1, 11, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [13, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 13, 13, 7, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7] 21 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 36, 37, 35, 38, 34, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237955 none COC1=CC(C=C2CC3=C(C=CC(OC)=C3F)C2=O)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 15, 1, 11, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 17, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 7, 7, 7, 7, 7, 17, 17, 17, 1, 1] 21 rigid atoms, others: [1, 2, 3, 4, 5, 38, 19, 20, 21, 22, 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, 36]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237955 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237955 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237955/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237955 Building REAL300000237956 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237956' /scratch/stefan/7769818/working/building/REAL300000237956 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237956 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237956/0 /scratch/stefan/7769818/working/building/REAL300000237956 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/956 `/scratch/stefan/7769818/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=C(F)C=C(C(=O)[O-])C=C3F)CC2=C1F) `REAL300000237956.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237956 none COC1=CC=C2C(=O)C(=CC3=C(F)C=C(C(=O)[O-])C=C3F)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 4, 4] 4 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237956 none COC1=CC=C2C(=O)C(=CC3=C(F)C=C(C(=O)[O-])C=C3F)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 15, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 4, 4, 1, 1] 4 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 21, 22, 23, 24, 33, 28, 29, 30] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 31]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237956 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237956 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237956/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237956 Building REAL300000237957 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237957' /scratch/stefan/7769818/working/building/REAL300000237957 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237957 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237957/0 /scratch/stefan/7769818/working/building/REAL300000237957 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/957 `/scratch/stefan/7769818/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=C(F)C=CC(C(=O)[O-])=C3F)CC2=C1F) `REAL300000237957.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237957 none COC1=CC=C2C(=O)C(=CC3=C(F)C=CC(C(=O)[O-])=C3F)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 1, 15, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 7, 7, 1, 1, 7, 7] 13 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237957 none COC1=CC=C2C(=O)C(=CC3=C(F)C=CC(C(=O)[O-])=C3F)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 1, 15, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 13, 13, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 1, 1] 13 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 21, 22, 23, 24, 33, 28, 29, 30] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 31]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237957 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237957 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237957/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237957 Building REAL300000237958 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237958' /scratch/stefan/7769818/working/building/REAL300000237958 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237958 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237958/0 /scratch/stefan/7769818/working/building/REAL300000237958 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/958 `/scratch/stefan/7769818/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CSC(C(=O)[O-])=C3)CC2=C1F) `REAL300000237958.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237958 none COC1=CC=C2C(=O)C(=CC3=CSC(C(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 7, 7] 7 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237958 none COC1=CC=C2C(=O)C(=CC3=CSC(C(=O)[O-])=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 1, 1] 7 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 25, 26, 27, 30, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 28, 29]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237958 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237958 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237958/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237958 Building REAL300000237959 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237959' /scratch/stefan/7769818/working/building/REAL300000237959 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237959 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237959/0 /scratch/stefan/7769818/working/building/REAL300000237959 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/959 `/scratch/stefan/7769818/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=C2CC3=C(C=CC(OC)=C3F)C2=O)=CC=C1OCC(=O)[O-]) `REAL300000237959.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237959 none CCOC1=CC(C=C2CC3=C(C=CC(OC)=C3F)C2=O)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 15, 1, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 5, 5, 5, 5, 36, 120, 159, 159, 67, 67, 67, 67, 67, 5, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 120, 120] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 38, 37] set([0, 1, 2, 3, 4, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237959 none CCOC1=CC(C=C2CC3=C(C=CC(OC)=C3F)C2=O)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 15, 1, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 5, 5, 13, 5, 5, 5, 5, 1, 1, 1, 1, 9, 44, 79, 79, 33, 33, 33, 33, 33, 1, 5, 5, 5, 5, 5, 13, 13, 13, 1, 1, 44, 44] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 42, 43, 20, 21, 22, 23] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237959 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237959 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237959/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237959 Building REAL300000237960 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237960' /scratch/stefan/7769818/working/building/REAL300000237960 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237960 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237960/0 /scratch/stefan/7769818/working/building/REAL300000237960 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/960 `/scratch/stefan/7769818/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC(F)=C(C(=O)[O-])C(F)=C3)CC2=C1F) `REAL300000237960.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237960 none COC1=CC=C2C(=O)C(=CC3=CC(F)=C(C(=O)[O-])C(F)=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 4, 4, 4, 1, 1, 4, 4] 5 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237960 none COC1=CC=C2C(=O)C(=CC3=CC(F)=C(C(=O)[O-])C(F)=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 15, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 2, 3, 5, 5, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 4, 4, 1, 1] 5 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 21, 22, 23, 24, 33, 28, 29, 30] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 31]) total number of confs: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237960 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237960 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237960/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237960 Building REAL300000237961 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237961' /scratch/stefan/7769818/working/building/REAL300000237961 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237961 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237961/0 /scratch/stefan/7769818/working/building/REAL300000237961 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/961 `/scratch/stefan/7769818/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC4=C(C=C(C(=O)[O-])N4)O3)CC2=C1F) `REAL300000237961.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237961 none COC1=CC=C2C(=O)C(=CC3=CC4=C(C=C(C(=O)[O-])N4)O3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8] 8 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237961 none COC1=CC=C2C(=O)C(=CC3=CC4=C(C=C(C(=O)[O-])N4)O3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 8, 8, 8, 1, 1] 8 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 21, 22, 23, 24, 28, 29, 30] set([0, 32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 31]) total number of confs: 12 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237961 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237961 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237961/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237961 Building REAL300000237962 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237962' /scratch/stefan/7769818/working/building/REAL300000237962 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237962 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237962/0 /scratch/stefan/7769818/working/building/REAL300000237962 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/962 `/scratch/stefan/7769818/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C4OC(C(=O)[O-])=CC4=C3)CC2=C1F) `REAL300000237962.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237962 none COC1=CC=C2C(=O)C(=CC3=CC=C4OC(C(=O)[O-])=CC4=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7] 7 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237962 none COC1=CC=C2C(=O)C(=CC3=CC=C4OC(C(=O)[O-])=CC4=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 37, 25, 22, 23, 24, 36, 29, 30, 31] set([0, 32, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237962 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237962 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237962/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237962 Building REAL300000237963 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237963' /scratch/stefan/7769818/working/building/REAL300000237963 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237963 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237963/0 /scratch/stefan/7769818/working/building/REAL300000237963 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/963 `/scratch/stefan/7769818/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=CN4C(C(=O)[O-])=CN=C34)CC2=C1F) `REAL300000237963.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237963 none COC1=CC=C2C(=O)C(=CC3=CC=CN4C(C(=O)[O-])=CN=C34)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6] 6 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 36, 37, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237963 none COC1=CC=C2C(=O)C(=CC3=CC=CN4C(C(=O)[O-])=CN=C34)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 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, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 6, 6, 6, 6, 1, 1] 6 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 37, 25, 22, 23, 24, 36, 29, 30, 31] set([0, 32, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237963 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237963 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237963/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237963 Building REAL300000237964 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237964' /scratch/stefan/7769818/working/building/REAL300000237964 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237964 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237964/0 /scratch/stefan/7769818/working/building/REAL300000237964 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/964 `/scratch/stefan/7769818/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=NC4=CC=CC=C4C(C(=O)[O-])=C3C)CC2=C1F) `REAL300000237964.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237964 none COC1=CC=C2C(=O)C(=CC3=NC4=CC=CC=C4C(C(=O)[O-])=C3C)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.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', '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, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 7, 7] 7 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237964 none COC1=CC=C2C(=O)C(=CC3=NC4=CC=CC=C4C(C(=O)[O-])=C3C)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.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', '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, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 41, 24, 25, 26, 27, 42, 31] set([0, 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: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237964 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237964 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237964/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237964 Building REAL300000237965 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237965' /scratch/stefan/7769818/working/building/REAL300000237965 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237965 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237965/0 /scratch/stefan/7769818/working/building/REAL300000237965 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/965 `/scratch/stefan/7769818/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CN=C4C=CC(C(=O)[O-])=CN34)CC2=C1F) `REAL300000237965.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237965 none COC1=CC=C2C(=O)C(=CC3=CN=C4C=CC(C(=O)[O-])=CN34)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 7, 7] 7 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237965 none COC1=CC=C2C(=O)C(=CC3=CN=C4C=CC(C(=O)[O-])=CN34)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 1, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 37, 25, 22, 23, 24, 36, 29, 30, 31] set([0, 32, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237965 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237965 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237965/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237965 Building REAL300000237966 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237966' /scratch/stefan/7769818/working/building/REAL300000237966 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237966 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237966/0 /scratch/stefan/7769818/working/building/REAL300000237966 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/966 `/scratch/stefan/7769818/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(N4C=NC(C(=O)[O-])=C4)C=C3)CC2=C1F) `REAL300000237966.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237966 none COC1=CC=C2C(=O)C(=CC3=CC=C(N4C=NC(C(=O)[O-])=C4)C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 1, 1, 8, 8, 1, 1, 4, 4] 12 rigid atoms, others: [34, 35, 38, 39, 9, 10, 11, 12, 13, 14, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41]) total number of confs: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237966 none COC1=CC=C2C(=O)C(=CC3=CC=C(N4C=NC(C(=O)[O-])=C4)C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8, 1, 1, 8, 8, 12, 12] 12 rigid atoms, others: [36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 44 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: REAL300000237966 none COC1=CC=C2C(=O)C(=CC3=CC=C(N4C=NC(C(=O)[O-])=C4)C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 12, 12, 12, 12, 12, 4, 4, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 4, 4, 12, 12, 4, 4, 1, 1] 12 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 40, 41, 24, 25, 26, 27, 31] set([0, 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: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237966 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237966 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237966/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237966 Building REAL300000237967 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237967' /scratch/stefan/7769818/working/building/REAL300000237967 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237967 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237967/0 /scratch/stefan/7769818/working/building/REAL300000237967 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/967 `/scratch/stefan/7769818/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=CC(C(=O)[O-])=C3F)CC2=C1F) `REAL300000237967.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237967 none COC1=CC=C2C(=O)C(=CC3=CC=CC(C(=O)[O-])=C3F)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 6, 6, 1, 1, 1, 6, 6] 11 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237967 none COC1=CC=C2C(=O)C(=CC3=CC=CC(C(=O)[O-])=C3F)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 6, 6, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 6, 6, 6, 1, 1] 11 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 20, 21, 22, 23, 33, 27, 28, 29] set([0, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 30, 31]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237967 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237967 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237967/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237967 Building REAL300000237968 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237968' /scratch/stefan/7769818/working/building/REAL300000237968 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237968 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237968/0 /scratch/stefan/7769818/working/building/REAL300000237968 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/968 `/scratch/stefan/7769818/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(OCC(=O)[O-])C(Cl)=C3)CC2=C1F) `REAL300000237968.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237968 none COC1=CC=C2C(=O)C(=CC3=CC=C(OCC(=O)[O-])C(Cl)=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 10, 42, 64, 64, 1, 1, 1, 7, 7, 7, 7, 19, 19, 19, 7, 7, 7, 1, 1, 42, 42, 1, 7, 7] 108 rigid atoms, others: [32, 33, 36, 9, 10, 11, 12, 13, 14, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 37, 38]) total number of confs: 243 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237968 none COC1=CC=C2C(=O)C(=CC3=CC=C(OCC(=O)[O-])C(Cl)=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.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.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 2, 6, 42, 108, 108, 108, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 7, 108, 108, 7, 1, 1] 108 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 37, 22, 23, 24, 25, 38, 29, 30, 31] set([0, 32, 34, 35, 36, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28]) total number of confs: 344 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237968 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237968 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237968/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237968 Building REAL300000237969 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237969' /scratch/stefan/7769818/working/building/REAL300000237969 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237969 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237969/0 /scratch/stefan/7769818/working/building/REAL300000237969 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/969 `/scratch/stefan/7769818/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=CC=C4C(=O)[O-])C=C3)CC2=C1F) `REAL300000237969.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237969 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=CC=C4C(=O)[O-])C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 9, 9, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 1, 1, 7, 7, 6, 7, 1, 1, 4, 4] 13 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 41, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 43, 44]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237969 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=CC=C4C(=O)[O-])C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 11, 11, 11, 11, 13, 13, 13, 11, 11, 11, 7, 7, 1, 1, 1, 1, 7, 7, 11, 11] 13 rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44]) total number of confs: 48 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: REAL300000237969 none COC1=CC=C2C(=O)C(=CC3=CC=C(C4=CC=CC=C4C(=O)[O-])C=C3)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 10, 12, 12, 12, 13, 13, 4, 4, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 4, 4, 12, 12, 12, 12, 4, 4, 1, 1] 13 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 9, 10, 7, 44, 34, 43, 25, 26, 27, 28] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237969 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237969 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237969/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237969 Building REAL300000237970 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237970' /scratch/stefan/7769818/working/building/REAL300000237970 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237970 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237970/0 /scratch/stefan/7769818/working/building/REAL300000237970 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/970 `/scratch/stefan/7769818/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=C1CC2=C(C=CC(OC)=C2F)C1=O) `REAL300000237970.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237970 none COC1=CC(C(=O)[O-])=CC=C1C=C1CC2=C(C=CC(OC)=C2F)C1=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', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.2', 'O.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, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 15, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 4] 9 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 37, 20, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 22 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237970 none COC1=CC(C(=O)[O-])=CC=C1C=C1CC2=C(C=CC(OC)=C2F)C1=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', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.2', 'O.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, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 15, 1, 11, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 6, 6, 6, 6, 4, 4, 4, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 9] 9 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]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237970 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237970 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237970/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237970 Building REAL300000237971 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237971' /scratch/stefan/7769818/working/building/REAL300000237971 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237971 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237971/0 /scratch/stefan/7769818/working/building/REAL300000237971 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/971 `/scratch/stefan/7769818/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=O)C(=CC3=C4C=C(C(=O)[O-])SC4=CC=C3F)CC2=C1F) `REAL300000237971.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237971 none COC1=CC=C2C(=O)C(=CC3=C4C=C(C(=O)[O-])SC4=CC=C3F)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7] 7 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 36, 37, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237971 none COC1=CC=C2C(=O)C(=CC3=C4C=C(C(=O)[O-])SC4=CC=C3F)CC2=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 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 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 7, 1, 1] 7 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 36, 37, 30, 31] set([0, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237971 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237971 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237971/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237971 Building REAL300000237972 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237972' /scratch/stefan/7769818/working/building/REAL300000237972 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237972 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237972/0 /scratch/stefan/7769818/working/building/REAL300000237972 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/972 `/scratch/stefan/7769818/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(OCC(=O)[O-])C(OC)=C2)NC1=O) `REAL300000237972.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237972 none COC1=CN=C(C=CC2=CC=C(OCC(=O)[O-])C(OC)=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 12, 5, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 5, 5, 1, 1, 1, 1, 1, 1, 9, 24, 37, 37, 1, 1, 3, 1, 26, 26, 26, 46, 46, 46, 26, 5, 5, 1, 1, 24, 24, 3, 3, 3, 1, 26] 201 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 17, 18, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 38]) total number of confs: 195 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237972 none COC1=CN=C(C=CC2=CC=C(OCC(=O)[O-])C(OC)=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 12, 5, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 26, 26, 26, 26, 96, 170, 176, 176, 26, 26, 48, 26, 1, 1, 1, 3, 3, 3, 1, 9, 9, 26, 26, 170, 170, 48, 48, 48, 26, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 38, 21, 22, 23, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 543 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237972 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237972/1 /scratch/stefan/7769818/working/building/REAL300000237972 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/973 `/scratch/stefan/7769818/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(OCC(=O)[O-])C(OC)=C2)[N-]C1=O) `REAL300000237972.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237972 none COC1=CN=C(C=CC2=CC=C(OCC(=O)[O-])C(OC)=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 12, 5, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 9, 28, 49, 49, 1, 1, 3, 1, 21, 21, 21, 39, 39, 39, 21, 5, 5, 1, 1, 28, 28, 4, 4, 4, 1] 201 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 17, 18, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 235 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237972 none COC1=CN=C(C=CC2=CC=C(OCC(=O)[O-])C(OC)=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 12, 5, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 95, 170, 191, 191, 21, 21, 40, 21, 1, 1, 1, 3, 3, 3, 1, 6, 6, 21, 21, 170, 170, 40, 40, 40, 21] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 572 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237972 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237972 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237972/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237972/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237972 Building REAL300000237973 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237973' /scratch/stefan/7769818/working/building/REAL300000237973 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237973 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237973/0 /scratch/stefan/7769818/working/building/REAL300000237973 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/974 `/scratch/stefan/7769818/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(OCC(=O)[O-])C=C2)NC1=O) `REAL300000237973.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237973 none COC1=CN=C(C=CC2=CC=C(OCC(=O)[O-])C=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 1, 1, 6, 26, 43, 43, 1, 1, 23, 23, 23, 45, 45, 45, 23, 4, 4, 1, 1, 27, 27, 1, 1, 23] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 34]) total number of confs: 210 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237973 none COC1=CN=C(C=CC2=CC=C(OCC(=O)[O-])C=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 23, 23, 11, 14, 74, 197, 201, 201, 23, 23, 1, 1, 1, 3, 3, 3, 1, 11, 11, 23, 23, 197, 197, 23, 23, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 19, 20, 21, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 698 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237973 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237973/1 /scratch/stefan/7769818/working/building/REAL300000237973 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/975 `/scratch/stefan/7769818/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(OCC(=O)[O-])C=C2)[N-]C1=O) `REAL300000237973.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237973 none COC1=CN=C(C=CC2=CC=C(OCC(=O)[O-])C=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [46, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 1, 1, 6, 26, 50, 50, 1, 1, 23, 23, 23, 46, 46, 46, 23, 4, 4, 1, 1, 26, 26, 1, 1] 178 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 223 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237973 none COC1=CN=C(C=CC2=CC=C(OCC(=O)[O-])C=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 23, 23, 11, 11, 71, 169, 179, 179, 23, 23, 1, 1, 1, 4, 4, 4, 1, 11, 11, 23, 23, 169, 169, 23, 23] 179 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 613 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237973 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237973 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237973/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237973/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237973 Building REAL300000237974 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237974' /scratch/stefan/7769818/working/building/REAL300000237974 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237974 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237974/0 /scratch/stefan/7769818/working/building/REAL300000237974 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/976 `/scratch/stefan/7769818/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(OCCC(=O)[O-])C=C2)NC1=O) `REAL300000237974.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237974 none COC1=CN=C(C=CC2=CC=C(OCCC(=O)[O-])C=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 1, 1, 6, 22, 30, 47, 39, 1, 1, 21, 21, 21, 46, 46, 46, 21, 4, 4, 1, 1, 22, 23, 29, 29, 1, 1, 21] 201 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 37]) total number of confs: 225 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237974 none COC1=CN=C(C=CC2=CC=C(OCCC(=O)[O-])C=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 21, 21, 11, 14, 70, 147, 168, 201, 186, 21, 21, 1, 1, 1, 3, 3, 3, 1, 11, 11, 21, 21, 147, 147, 168, 168, 21, 21, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 26, 37] 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, 34, 35, 36]) total number of confs: 748 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237974 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237974/1 /scratch/stefan/7769818/working/building/REAL300000237974 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/977 `/scratch/stefan/7769818/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(OCCC(=O)[O-])C=C2)[N-]C1=O) `REAL300000237974.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237974 none COC1=CN=C(C=CC2=CC=C(OCCC(=O)[O-])C=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 22, 22, 22, 22, 4, 4, 1, 1, 1, 1, 1, 1, 6, 24, 35, 49, 43, 1, 1, 22, 22, 22, 44, 44, 44, 22, 4, 4, 1, 1, 24, 24, 34, 34, 1, 1] 201 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 242 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237974 none COC1=CN=C(C=CC2=CC=C(OCCC(=O)[O-])C=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 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, 12, 12, 22, 22, 12, 12, 79, 163, 185, 201, 190, 22, 22, 1, 1, 1, 4, 4, 4, 1, 12, 12, 22, 22, 163, 163, 185, 185, 22, 22] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 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, 34, 35, 36]) total number of confs: 721 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237974 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237974 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237974/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237974/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237974 Building REAL300000237975 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237975' /scratch/stefan/7769818/working/building/REAL300000237975 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237975 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237975/0 /scratch/stefan/7769818/working/building/REAL300000237975 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/978 `/scratch/stefan/7769818/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=CC(OC(C)C(=O)[O-])=C2)NC1=O) `REAL300000237975.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237975 none COC1=CN=C(C=CC2=CC=CC(OC(C)C(=O)[O-])=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 32, 32, 32, 32, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 23, 23, 31, 31, 1, 32, 32, 32, 63, 63, 63, 32, 5, 5, 1, 1, 1, 23, 23, 23, 23, 1, 32] 201 rigid atoms, others: [36, 7, 8, 9, 10, 11, 12, 13, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 37]) total number of confs: 198 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237975 none COC1=CN=C(C=CC2=CC=CC(OC(C)C(=O)[O-])=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 32, 32, 32, 32, 32, 120, 184, 184, 201, 201, 32, 1, 1, 1, 4, 4, 4, 1, 11, 11, 32, 32, 32, 184, 184, 184, 184, 32, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 26, 37] 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, 34, 35, 36]) total number of confs: 587 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237975 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237975/1 /scratch/stefan/7769818/working/building/REAL300000237975 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/979 `/scratch/stefan/7769818/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=CC(OC(C)C(=O)[O-])=C2)[N-]C1=O) `REAL300000237975.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237975 none COC1=CN=C(C=CC2=CC=CC(OC(C)C(=O)[O-])=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [71, 36, 36, 35, 35, 6, 6, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18, 30, 30, 1, 36, 36, 36, 71, 71, 71, 36, 6, 6, 1, 1, 1, 18, 18, 18, 18, 1] 201 rigid atoms, others: [36, 7, 8, 9, 10, 11, 12, 13, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 213 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237975 none COC1=CN=C(C=CC2=CC=CC(OC(C)C(=O)[O-])=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 11, 11, 36, 36, 35, 36, 36, 107, 159, 159, 201, 201, 36, 1, 1, 1, 4, 4, 4, 1, 11, 11, 36, 36, 35, 159, 159, 159, 159, 36] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 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, 34, 35, 36]) total number of confs: 593 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237975 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237975 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237975/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237975/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237975 Building REAL300000237976 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237976' /scratch/stefan/7769818/working/building/REAL300000237976 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237976 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237976/0 /scratch/stefan/7769818/working/building/REAL300000237976 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/980 `/scratch/stefan/7769818/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=CC(OCCC(=O)[O-])=C2)NC1=O) `REAL300000237976.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237976 none COC1=CN=C(C=CC2=CC=CC(OCCC(=O)[O-])=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 33, 33, 33, 33, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 11, 21, 29, 29, 1, 33, 33, 33, 64, 64, 64, 33, 5, 5, 1, 1, 1, 11, 11, 21, 21, 1, 33] 201 rigid atoms, others: [36, 7, 8, 9, 10, 11, 12, 13, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 37]) total number of confs: 205 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237976 none COC1=CN=C(C=CC2=CC=CC(OCCC(=O)[O-])=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 33, 33, 33, 33, 33, 108, 118, 167, 201, 201, 33, 1, 1, 1, 3, 3, 3, 1, 12, 12, 33, 33, 33, 118, 118, 167, 167, 33, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 26, 37] 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, 34, 35, 36]) total number of confs: 617 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237976 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237976/1 /scratch/stefan/7769818/working/building/REAL300000237976 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/981 `/scratch/stefan/7769818/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=CC(OCCC(=O)[O-])=C2)[N-]C1=O) `REAL300000237976.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237976 none COC1=CN=C(C=CC2=CC=CC(OCCC(=O)[O-])=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [53, 30, 30, 30, 30, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 10, 24, 44, 44, 1, 30, 30, 30, 53, 53, 53, 30, 5, 5, 1, 1, 1, 10, 10, 24, 24, 1] 201 rigid atoms, others: [36, 7, 8, 9, 10, 11, 12, 13, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 247 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237976 none COC1=CN=C(C=CC2=CC=CC(OCCC(=O)[O-])=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 10, 10, 30, 30, 30, 30, 30, 87, 132, 189, 201, 201, 30, 1, 1, 1, 3, 3, 3, 1, 10, 10, 30, 30, 30, 132, 132, 189, 189, 30] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 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, 34, 35, 36]) total number of confs: 753 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237976 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237976 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237976/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237976/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237976 Building REAL300000237977 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237977' /scratch/stefan/7769818/working/building/REAL300000237977 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237977 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237977/0 /scratch/stefan/7769818/working/building/REAL300000237977 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/982 `/scratch/stefan/7769818/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)NC1=O) `REAL300000237977.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237977 none COC1=CN=C(C=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [67, 39, 39, 39, 39, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 7, 17, 17, 17, 17, 17, 17, 21, 21, 1, 39, 39, 39, 67, 67, 67, 39, 7, 6, 1, 1, 1, 7, 7, 17, 17, 17, 17, 1, 39] 192 rigid atoms, others: [34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 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, 44]) total number of confs: 155 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237977 none COC1=CN=C(C=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [192, 168, 168, 168, 168, 43, 43, 17, 17, 16, 17, 17, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 168, 168, 168, 192, 192, 192, 168, 43, 43, 16, 17, 17, 5, 5, 1, 1, 1, 1, 17, 168] 192 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 322 number of broken/clashed sets: 32 ./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: REAL300000237977 none COC1=CN=C(C=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 13, 13, 39, 39, 39, 39, 39, 67, 88, 168, 168, 168, 168, 168, 168, 192, 192, 39, 1, 1, 1, 4, 4, 4, 1, 13, 13, 39, 39, 39, 88, 88, 168, 168, 168, 168, 39, 1] 192 rigid atoms, others: [1, 2, 3, 4, 5, 6, 44, 25, 26, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 458 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237977 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237977/1 /scratch/stefan/7769818/working/building/REAL300000237977 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/983 `/scratch/stefan/7769818/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)[N-]C1=O) `REAL300000237977.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237977 none COC1=CN=C(C=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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: [44, 23, 23, 23, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 4, 9, 9, 8, 9, 9, 9, 11, 11, 1, 23, 23, 23, 44, 44, 44, 23, 5, 5, 1, 1, 1, 4, 4, 9, 9, 8, 9, 1] 93 rigid atoms, others: [34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 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: 102 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237977 none COC1=CN=C(C=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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, 77, 77, 77, 77, 24, 24, 9, 9, 9, 9, 9, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 77, 77, 77, 93, 93, 93, 77, 24, 24, 9, 8, 9, 4, 4, 1, 1, 1, 1, 9] 93 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43]) total number of confs: 176 number of broken/clashed sets: 11 ./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: REAL300000237977 none COC1=CN=C(C=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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, 10, 10, 23, 23, 23, 23, 23, 27, 37, 77, 77, 77, 77, 77, 77, 93, 93, 23, 1, 1, 1, 4, 4, 4, 1, 10, 10, 23, 23, 23, 37, 37, 77, 77, 77, 77, 23] 93 rigid atoms, others: [1, 2, 3, 4, 5, 6, 25, 26, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 229 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237977 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237977 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237977/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237977/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237977 Building REAL300000237978 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237978' /scratch/stefan/7769818/working/building/REAL300000237978 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237978 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237978/0 /scratch/stefan/7769818/working/building/REAL300000237978 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/984 `/scratch/stefan/7769818/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)NC1=O) `REAL300000237978.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237978 none COC1=CN=C(C=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 28, 28, 28, 28, 4, 4, 1, 1, 1, 1, 1, 1, 2, 6, 21, 21, 21, 21, 21, 37, 37, 21, 1, 1, 28, 28, 28, 60, 60, 60, 28, 4, 4, 1, 1, 6, 6, 21, 21, 21, 21, 1, 1, 28] 201 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 189 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237978 none COC1=CN=C(C=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 181, 181, 181, 181, 44, 44, 21, 21, 21, 21, 11, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 181, 181, 181, 201, 201, 201, 181, 44, 44, 21, 21, 9, 9, 1, 2, 2, 2, 21, 20, 181] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 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: 362 number of broken/clashed sets: 18 ./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: REAL300000237978 none COC1=CN=C(C=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 13, 28, 28, 28, 28, 44, 54, 181, 181, 181, 181, 181, 201, 201, 181, 28, 28, 1, 1, 1, 3, 3, 3, 1, 13, 13, 28, 28, 54, 54, 181, 181, 181, 181, 28, 28, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 44, 25, 26, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 388 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237978 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237978/1 /scratch/stefan/7769818/working/building/REAL300000237978 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/985 `/scratch/stefan/7769818/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)[N-]C1=O) `REAL300000237978.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237978 none COC1=CN=C(C=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 15, 15, 15, 15, 4, 4, 1, 1, 1, 1, 1, 1, 2, 6, 29, 29, 29, 29, 29, 51, 51, 29, 1, 1, 15, 15, 15, 33, 33, 33, 15, 4, 4, 1, 1, 6, 6, 29, 29, 29, 29, 1, 1] 201 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 190 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237978 none COC1=CN=C(C=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 141, 141, 141, 141, 55, 55, 29, 29, 29, 29, 17, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 29, 29, 141, 141, 141, 201, 201, 201, 141, 55, 55, 29, 29, 9, 9, 1, 2, 2, 2, 29, 29] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 423 number of broken/clashed sets: 51 ./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: REAL300000237978 none COC1=CN=C(C=CC2=CC=C(OCC3=CC(C)=C(C(=O)[O-])O3)C=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 15, 15, 11, 11, 27, 46, 141, 141, 141, 141, 141, 201, 201, 141, 15, 15, 1, 1, 1, 4, 4, 4, 1, 11, 11, 15, 15, 46, 46, 141, 141, 141, 141, 15, 15] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 25, 26, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 537 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237978 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237978 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237978/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237978/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237978 Building REAL300000237979 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237979' /scratch/stefan/7769818/working/building/REAL300000237979 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237979 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237979/0 /scratch/stefan/7769818/working/building/REAL300000237979 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/986 `/scratch/stefan/7769818/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)NC1=O) `REAL300000237979.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237979 none COC1=CN=C(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 4, 7, 6, 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: [38, 30, 30, 30, 30, 9, 9, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 7, 6, 7, 7, 1, 30, 30, 30, 38, 38, 38, 30, 9, 9, 1, 1, 7, 7, 7, 7, 30] 88 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237979 none COC1=CN=C(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 4, 7, 6, 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, 88, 88, 88, 88, 34, 34, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 88, 88, 88, 88, 88, 88, 88, 34, 34, 7, 7, 1, 1, 1, 1, 88] 88 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 152 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: REAL300000237979 none COC1=CN=C(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 4, 7, 6, 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: [3, 1, 1, 1, 1, 1, 1, 12, 12, 30, 30, 30, 30, 88, 88, 30, 30, 88, 88, 88, 88, 30, 1, 1, 1, 4, 4, 4, 1, 12, 12, 30, 30, 88, 88, 88, 88, 1] 88 rigid atoms, others: [1, 2, 3, 4, 5, 6, 22, 23, 24, 28, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 402 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237979 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237979/1 /scratch/stefan/7769818/working/building/REAL300000237979 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/987 `/scratch/stefan/7769818/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)[N-]C1=O) `REAL300000237979.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237979 none COC1=CN=C(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 3, 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: [44, 32, 32, 31, 31, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 7, 6, 7, 7, 1, 32, 32, 32, 44, 44, 44, 32, 12, 12, 1, 1, 7, 7, 7, 7] 88 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 108 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237979 none COC1=CN=C(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 3, 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, 88, 88, 88, 88, 42, 42, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 88, 88, 88, 88, 88, 88, 88, 42, 42, 7, 7, 1, 1, 1, 1] 88 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) 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: REAL300000237979 none COC1=CN=C(C=CC2=CC=C(C3=CC=C(C(=O)[O-])C=C3)O2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 11, 11, 32, 32, 32, 32, 88, 88, 32, 32, 88, 88, 88, 88, 32, 1, 1, 1, 4, 4, 4, 1, 11, 12, 32, 32, 88, 88, 88, 88] 88 rigid atoms, others: [1, 2, 3, 4, 5, 6, 22, 23, 24, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237979 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237979 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237979/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237979/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237979 Building REAL300000237980 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237980' /scratch/stefan/7769818/working/building/REAL300000237980 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237980 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237980/0 /scratch/stefan/7769818/working/building/REAL300000237980 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/988 `/scratch/stefan/7769818/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)NC1=O) `REAL300000237980.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237980 none COC1=CN=C(C=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 31, 31, 31, 31, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 5, 15, 15, 15, 15, 15, 15, 15, 15, 1, 31, 31, 31, 43, 43, 43, 31, 5, 5, 1, 1, 1, 5, 5, 15, 15, 15, 15, 1, 31] 201 rigid atoms, others: [34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 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, 44]) total number of confs: 89 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237980 none COC1=CN=C(C=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 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, 48, 48, 15, 15, 14, 15, 15, 9, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 15, 201, 201, 201, 201, 201, 201, 201, 48, 48, 14, 15, 15, 7, 7, 1, 1, 1, 1, 15, 201] 201 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 331 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: REAL300000237980 none COC1=CN=C(C=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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 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, 10, 10, 31, 31, 31, 31, 31, 59, 63, 201, 201, 201, 201, 201, 201, 201, 201, 31, 1, 1, 1, 3, 3, 3, 1, 10, 10, 31, 31, 31, 63, 63, 201, 201, 201, 201, 31, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 44, 25, 26, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 321 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237980 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237980/1 /scratch/stefan/7769818/working/building/REAL300000237980 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/989 `/scratch/stefan/7769818/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)[N-]C1=O) `REAL300000237980.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237980 none COC1=CN=C(C=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 25, 25, 25, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 15, 15, 15, 15, 15, 16, 16, 15, 1, 25, 25, 25, 36, 36, 36, 25, 5, 5, 1, 1, 1, 3, 3, 16, 15, 15, 16, 1] 201 rigid atoms, others: [34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 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: 86 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237980 none COC1=CN=C(C=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 57, 57, 15, 15, 15, 15, 15, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 15, 201, 201, 201, 201, 201, 201, 201, 57, 57, 15, 15, 16, 8, 8, 1, 1, 1, 1, 15] 201 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43]) total number of confs: 353 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: REAL300000237980 none COC1=CN=C(C=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 11, 11, 25, 25, 25, 25, 25, 43, 43, 201, 201, 201, 201, 201, 201, 201, 201, 25, 1, 1, 1, 3, 3, 3, 1, 11, 11, 25, 25, 25, 43, 43, 201, 201, 201, 201, 25] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 25, 26, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 280 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237980 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237980 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237980/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237980/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237980 Building REAL300000237981 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237981' /scratch/stefan/7769818/working/building/REAL300000237981 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237981 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237981/0 /scratch/stefan/7769818/working/building/REAL300000237981 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/990 `/scratch/stefan/7769818/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=C([N+](=O)[O-])C=C(OCC(=O)[O-])C(OC)=C2)NC1=O) `REAL300000237981.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237981 none COC1=CN=C(C=CC2=C([N+](=O)[O-])C=C(OCC(=O)[O-])C(OC)=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 1, 12, 5, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 10, 36, 51, 51, 1, 1, 4, 1, 23, 23, 23, 39, 39, 39, 23, 5, 5, 1, 36, 36, 4, 4, 4, 1, 23] 201 rigid atoms, others: [33, 7, 8, 9, 10, 39, 13, 14, 15, 20, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 16, 17, 18, 19, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 40]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237981 none COC1=CN=C(C=CC2=C([N+](=O)[O-])C=C(OCC(=O)[O-])C(OC)=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 1, 12, 5, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 23, 23, 23, 23, 23, 23, 23, 99, 190, 195, 195, 23, 23, 43, 23, 1, 1, 1, 3, 3, 3, 1, 12, 12, 23, 190, 190, 43, 43, 43, 23, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 24, 25, 26, 30] set([0, 7, 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]) total number of confs: 593 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237981 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237981/1 /scratch/stefan/7769818/working/building/REAL300000237981 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/991 `/scratch/stefan/7769818/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=C([N+](=O)[O-])C=C(OCC(=O)[O-])C(OC)=C2)[N-]C1=O) `REAL300000237981.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237981 none COC1=CN=C(C=CC2=C([N+](=O)[O-])C=C(OCC(=O)[O-])C(OC)=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 1, 12, 5, 1, 8, 1, 11, 7, 7, 7, 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, 3, 7, 7, 2, 2, 7, 3, 7, 7, 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: [41, 23, 23, 23, 23, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 29, 64, 64, 1, 1, 3, 1, 23, 23, 23, 41, 41, 41, 23, 5, 5, 1, 29, 29, 4, 4, 4, 1] 201 rigid atoms, others: [33, 7, 8, 9, 10, 39, 13, 14, 15, 20, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 16, 17, 18, 19, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237981 none COC1=CN=C(C=CC2=C([N+](=O)[O-])C=C(OCC(=O)[O-])C(OC)=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 1, 12, 5, 1, 8, 1, 11, 7, 7, 7, 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, 3, 7, 7, 2, 2, 7, 3, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 9, 9, 23, 23, 23, 23, 23, 23, 23, 101, 179, 195, 195, 23, 23, 47, 23, 1, 1, 1, 3, 3, 3, 1, 9, 9, 23, 179, 179, 47, 47, 47, 23] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 24, 25, 26, 30] set([0, 7, 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]) total number of confs: 625 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237981 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237981 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237981/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237981/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237981 Building REAL300000237982 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237982' /scratch/stefan/7769818/working/building/REAL300000237982 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237982 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237982/0 /scratch/stefan/7769818/working/building/REAL300000237982 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/992 `/scratch/stefan/7769818/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=CC(OCC(=O)[O-])=C2)NC1=O) `REAL300000237982.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237982 none COC1=CN=C(C=CC2=CC=CC(OCC(=O)[O-])=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 29, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 19, 30, 30, 1, 29, 29, 29, 53, 53, 53, 29, 5, 5, 1, 1, 1, 19, 19, 1, 29] 201 rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 34]) total number of confs: 177 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237982 none COC1=CN=C(C=CC2=CC=CC(OCC(=O)[O-])=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 29, 29, 29, 29, 29, 95, 178, 201, 201, 29, 1, 1, 1, 4, 4, 4, 1, 11, 11, 29, 29, 29, 178, 178, 29, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 19, 20, 21, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 673 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237982 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237982/1 /scratch/stefan/7769818/working/building/REAL300000237982 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/993 `/scratch/stefan/7769818/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=CC(OCC(=O)[O-])=C2)[N-]C1=O) `REAL300000237982.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237982 none COC1=CN=C(C=CC2=CC=CC(OCC(=O)[O-])=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [50, 29, 29, 29, 29, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 17, 30, 30, 1, 29, 29, 29, 50, 50, 50, 29, 5, 5, 1, 1, 1, 17, 17, 1] 115 rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 13, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32]) total number of confs: 174 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237982 none COC1=CN=C(C=CC2=CC=CC(OCC(=O)[O-])=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 3, 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, 10, 10, 29, 29, 29, 29, 29, 76, 99, 115, 115, 29, 1, 1, 1, 4, 4, 4, 1, 10, 10, 29, 29, 29, 99, 99, 29] 115 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 320 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237982 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237982 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237982/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237982/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237982 Building REAL300000237983 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237983' /scratch/stefan/7769818/working/building/REAL300000237983 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237983 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237983/0 /scratch/stefan/7769818/working/building/REAL300000237983 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/994 `/scratch/stefan/7769818/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)NC1=O) `REAL300000237983.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237983 none COC1=CN=C(C=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 4, 4, 1, 1, 1, 1, 1, 1, 2, 10, 23, 23, 29, 29, 23, 23, 23, 1, 1, 26, 26, 26, 58, 58, 58, 26, 4, 4, 1, 1, 10, 10, 23, 23, 1, 1, 26] 201 rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 40, 22, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 41]) total number of confs: 160 number of broken/clashed sets: 87 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237983 none COC1=CN=C(C=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 188, 188, 188, 188, 43, 43, 23, 23, 23, 23, 12, 6, 1, 1, 1, 1, 3, 3, 1, 1, 1, 23, 23, 188, 188, 188, 201, 201, 201, 188, 43, 43, 23, 23, 6, 6, 1, 1, 23, 23, 188] 201 rigid atoms, others: [37, 38, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 339 number of broken/clashed sets: 87 ./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: REAL300000237983 none COC1=CN=C(C=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 26, 26, 26, 26, 46, 120, 188, 188, 201, 201, 188, 188, 188, 26, 26, 1, 1, 1, 3, 3, 3, 1, 13, 13, 26, 26, 120, 120, 188, 188, 26, 26, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 41, 24, 25, 26, 30] set([0, 7, 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]) total number of confs: 570 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237983 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237983/1 /scratch/stefan/7769818/working/building/REAL300000237983 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/995 `/scratch/stefan/7769818/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)[N-]C1=O) `REAL300000237983.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237983 none COC1=CN=C(C=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 3, 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: [39, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 1, 1, 2, 10, 19, 19, 25, 25, 19, 19, 19, 1, 1, 19, 19, 19, 39, 39, 39, 19, 3, 3, 1, 1, 10, 10, 19, 19, 1, 1] 128 rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 40, 22, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 128 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237983 none COC1=CN=C(C=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 3, 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, 120, 120, 120, 120, 35, 35, 10, 10, 19, 19, 10, 6, 1, 1, 1, 1, 3, 3, 1, 1, 1, 19, 19, 120, 120, 120, 128, 128, 128, 120, 35, 35, 18, 19, 6, 6, 1, 1, 19, 19] 128 rigid atoms, others: [37, 38, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 274 number of broken/clashed sets: 37 ./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: REAL300000237983 none COC1=CN=C(C=CC2=CC=C(OCC3=C(C(=O)[O-])C=CO3)C=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 10, 10, 19, 19, 10, 10, 37, 71, 120, 120, 128, 128, 120, 120, 120, 19, 19, 1, 1, 1, 4, 4, 4, 1, 10, 10, 19, 19, 71, 71, 120, 120, 19, 19] 128 rigid atoms, others: [1, 2, 3, 4, 5, 6, 24, 25, 26, 30] set([0, 7, 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]) total number of confs: 367 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237983 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237983 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237983/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237983/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237983 Building REAL300000237984 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237984' /scratch/stefan/7769818/working/building/REAL300000237984 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237984 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237984/0 /scratch/stefan/7769818/working/building/REAL300000237984 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/996 `/scratch/stefan/7769818/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)NC1=O) `REAL300000237984.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237984 none COC1=CN=C(C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 1, 1, 10, 32, 32, 32, 41, 41, 1, 1, 18, 18, 18, 33, 33, 33, 18, 3, 3, 1, 1, 1, 1, 18] 201 rigid atoms, others: [32, 33, 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, 34]) total number of confs: 181 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237984 none COC1=CN=C(C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 18, 18, 10, 10, 90, 177, 177, 177, 201, 201, 18, 18, 1, 1, 1, 4, 4, 4, 1, 10, 10, 18, 18, 18, 18, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 21, 22, 23, 27] set([0, 7, 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: 666 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237984 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237984/1 /scratch/stefan/7769818/working/building/REAL300000237984 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/997 `/scratch/stefan/7769818/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)[N-]C1=O) `REAL300000237984.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237984 none COC1=CN=C(C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 1, 1, 12, 38, 38, 38, 67, 67, 1, 1, 19, 19, 19, 35, 35, 35, 19, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 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]) total number of confs: 276 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237984 none COC1=CN=C(C=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 11, 11, 19, 19, 11, 11, 92, 167, 167, 167, 201, 201, 19, 19, 1, 1, 1, 4, 4, 4, 1, 11, 11, 19, 19, 19, 19] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23, 27] set([0, 7, 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: 641 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237984 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237984 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237984/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237984/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237984 Building REAL300000237985 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237985' /scratch/stefan/7769818/working/building/REAL300000237985 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237985 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237985/0 /scratch/stefan/7769818/working/building/REAL300000237985 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/998 `/scratch/stefan/7769818/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)NC1=O) `REAL300000237985.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237985 none COC1=CN=C(C=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 5, 5, 1, 1, 1, 1, 1, 1, 7, 26, 36, 36, 1, 1, 1, 34, 34, 34, 67, 67, 67, 34, 5, 5, 1, 1, 26, 26, 1, 34] 201 rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34]) total number of confs: 226 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237985 none COC1=CN=C(C=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 34, 34, 34, 34, 124, 195, 201, 201, 34, 34, 34, 1, 1, 1, 3, 3, 3, 1, 11, 11, 34, 34, 195, 195, 34, 1] 201 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]) total number of confs: 528 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237985 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237985/1 /scratch/stefan/7769818/working/building/REAL300000237985 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/999 `/scratch/stefan/7769818/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)[N-]C1=O) `REAL300000237985.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237985 none COC1=CN=C(C=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 32, 32, 32, 32, 5, 5, 1, 1, 1, 1, 1, 1, 7, 27, 53, 53, 1, 1, 1, 32, 32, 32, 66, 66, 66, 32, 5, 5, 1, 1, 27, 27, 1] 201 rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 271 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237985 none COC1=CN=C(C=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 32, 32, 30, 31, 108, 188, 201, 201, 32, 32, 32, 1, 1, 1, 4, 4, 4, 1, 10, 10, 32, 32, 188, 188, 32] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 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]) total number of confs: 579 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237985 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237985 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237985/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237985/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237985 Building REAL300000237986 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237986' /scratch/stefan/7769818/working/building/REAL300000237986 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237986 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237986/0 /scratch/stefan/7769818/working/building/REAL300000237986 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1000 `/scratch/stefan/7769818/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=C3C=C(C(=O)[O-])OC3=C(OC)C=C2)NC1=O) `REAL300000237986.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237986 none COC1=CN=C(C=CC2=C3C=C(C(=O)[O-])OC3=C(OC)C=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 12, 5, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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, 42, 42, 42, 42, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 42, 42, 42, 60, 60, 60, 42, 10, 10, 1, 3, 3, 3, 1, 1, 42] 60 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 101 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237986 none COC1=CN=C(C=CC2=C3C=C(C(=O)[O-])OC3=C(OC)C=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 12, 5, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 4, 7, 6, 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, 12, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 60, 42, 42, 1, 1, 1, 4, 4, 4, 1, 12, 12, 42, 60, 60, 60, 42, 42, 1] 60 rigid atoms, others: [1, 2, 3, 4, 5, 6, 22, 23, 24, 28, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 107 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237986 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237986/1 /scratch/stefan/7769818/working/building/REAL300000237986 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1001 `/scratch/stefan/7769818/working/3D/1001' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=C3C=C(C(=O)[O-])OC3=C(OC)C=C2)[N-]C1=O) `REAL300000237986.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237986 none COC1=CN=C(C=CC2=C3C=C(C(=O)[O-])OC3=C(OC)C=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 12, 5, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 33, 33, 33, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 33, 33, 33, 49, 49, 49, 33, 9, 9, 1, 3, 3, 3, 1, 1] 49 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 86 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237986 none COC1=CN=C(C=CC2=C3C=C(C(=O)[O-])OC3=C(OC)C=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 12, 5, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 49, 33, 33, 1, 1, 1, 3, 3, 3, 1, 12, 12, 33, 49, 49, 49, 33, 33] 49 rigid atoms, others: [1, 2, 3, 4, 5, 6, 22, 23, 24, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 89 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237986 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237986 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237986/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237986/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237986 Building REAL300000237987 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237987' /scratch/stefan/7769818/working/building/REAL300000237987 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237987 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237987/0 /scratch/stefan/7769818/working/building/REAL300000237987 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1002 `/scratch/stefan/7769818/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(OCCC(=O)[O-])C(OC)=C2)NC1=O) `REAL300000237987.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237987 none COC1=CN=C(C=CC2=CC=C(OCCC(=O)[O-])C(OC)=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 29, 29, 29, 29, 5, 5, 1, 1, 1, 1, 1, 1, 8, 25, 25, 35, 34, 1, 1, 3, 1, 29, 29, 29, 49, 49, 49, 29, 5, 5, 1, 1, 25, 25, 25, 25, 3, 3, 3, 1, 29] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 40, 18, 19, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 199 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237987 none COC1=CN=C(C=CC2=CC=C(OCCC(=O)[O-])C(OC)=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 29, 29, 29, 29, 103, 128, 128, 182, 182, 29, 29, 46, 29, 1, 1, 1, 3, 3, 3, 1, 10, 10, 29, 29, 128, 128, 128, 128, 46, 46, 46, 29, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 41, 22, 23, 24, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 527 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237987 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237987/1 /scratch/stefan/7769818/working/building/REAL300000237987 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1003 `/scratch/stefan/7769818/working/3D/1003' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(OCCC(=O)[O-])C(OC)=C2)[N-]C1=O) `REAL300000237987.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237987 none COC1=CN=C(C=CC2=CC=C(OCCC(=O)[O-])C(OC)=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 18, 18, 18, 18, 5, 5, 1, 1, 1, 1, 1, 1, 7, 27, 27, 49, 48, 1, 1, 3, 1, 18, 18, 18, 33, 33, 33, 18, 5, 5, 1, 1, 27, 27, 27, 27, 3, 3, 3, 1] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 40, 18, 19, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 223 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237987 none COC1=CN=C(C=CC2=CC=C(OCCC(=O)[O-])C(OC)=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 12, 5, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 18, 18, 18, 18, 83, 152, 152, 195, 195, 18, 18, 39, 18, 1, 1, 1, 3, 3, 3, 1, 5, 5, 18, 18, 152, 152, 152, 152, 39, 39, 39, 18] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 22, 23, 24, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 653 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237987 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237987 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237987/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237987/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237987 Building REAL300000237988 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237988' /scratch/stefan/7769818/working/building/REAL300000237988 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237988 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237988/0 /scratch/stefan/7769818/working/building/REAL300000237988 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1004 `/scratch/stefan/7769818/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(C(=O)[O-])C=C2Cl)NC1=O) `REAL300000237988.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237988 none COC1=CN=C(C=CC2=CC=C(C(=O)[O-])C=C2Cl)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 14, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 14, 14, 14, 22, 22, 22, 14, 6, 6, 1, 1, 1, 14] 22 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 45 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237988 none COC1=CN=C(C=CC2=CC=C(C(=O)[O-])C=C2Cl)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 4, 4, 4, 1, 10, 10, 14, 14, 14, 1] 22 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 24, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 38 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237988 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237988/1 /scratch/stefan/7769818/working/building/REAL300000237988 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1005 `/scratch/stefan/7769818/working/3D/1005' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(C(=O)[O-])C=C2Cl)[N-]C1=O) `REAL300000237988.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237988 none COC1=CN=C(C=CC2=CC=C(C(=O)[O-])C=C2Cl)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 15, 15, 15, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 15, 15, 15, 27, 27, 27, 15, 8, 8, 1, 1, 1] 27 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 59 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237988 none COC1=CN=C(C=CC2=CC=C(C(=O)[O-])C=C2Cl)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 4, 4, 4, 1, 10, 10, 15, 15, 15] 27 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 24] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 39 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237988 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237988 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237988/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237988/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237988 Building REAL300000237989 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237989' /scratch/stefan/7769818/working/building/REAL300000237989 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237989 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237989/0 /scratch/stefan/7769818/working/building/REAL300000237989 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1006 `/scratch/stefan/7769818/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=CC(C(=O)[O-])=C2Cl)NC1=O) `REAL300000237989.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237989 none COC1=CN=C(C=CC2=CC=CC(C(=O)[O-])=C2Cl)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 30, 30, 30, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 30, 30, 30, 44, 44, 44, 30, 7, 7, 1, 1, 1, 30] 44 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 77 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237989 none COC1=CN=C(C=CC2=CC=CC(C(=O)[O-])=C2Cl)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 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: [3, 1, 1, 1, 1, 1, 1, 12, 12, 30, 30, 30, 30, 30, 32, 32, 30, 30, 1, 1, 1, 4, 4, 4, 1, 12, 12, 30, 30, 30, 1] 44 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 24, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237989 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237989/1 /scratch/stefan/7769818/working/building/REAL300000237989 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1007 `/scratch/stefan/7769818/working/3D/1007' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=CC(C(=O)[O-])=C2Cl)[N-]C1=O) `REAL300000237989.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237989 none COC1=CN=C(C=CC2=CC=CC(C(=O)[O-])=C2Cl)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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, 26, 26, 26, 26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 26, 26, 26, 41, 41, 41, 26, 9, 9, 1, 1, 1] 41 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 77 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237989 none COC1=CN=C(C=CC2=CC=CC(C(=O)[O-])=C2Cl)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 16, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 8, 8, 26, 26, 26, 26, 26, 34, 34, 26, 26, 1, 1, 1, 3, 3, 3, 1, 8, 8, 26, 26, 26] 41 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 24] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237989 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237989 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237989/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237989/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237989 Building REAL300000237990 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237990' /scratch/stefan/7769818/working/building/REAL300000237990 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237990 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237990/0 /scratch/stefan/7769818/working/building/REAL300000237990 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1008 `/scratch/stefan/7769818/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC(C(=O)[O-])=C(C)C=C2C)NC1=O) `REAL300000237990.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237990 none COC1=CN=C(C=CC2=CC(C(=O)[O-])=C(C)C=C2C)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 28, 28, 28, 28, 7, 7, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 28, 28, 28, 46, 46, 46, 28, 7, 7, 1, 2, 2, 2, 1, 2, 2, 2, 28] 46 rigid atoms, others: [32, 7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 94 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237990 none COC1=CN=C(C=CC2=CC(C(=O)[O-])=C(C)C=C2C)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 12, 12, 28, 28, 28, 46, 46, 28, 28, 28, 28, 28, 1, 1, 1, 4, 4, 4, 1, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 1] 46 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 25, 36] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237990 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237990/1 /scratch/stefan/7769818/working/building/REAL300000237990 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1009 `/scratch/stefan/7769818/working/3D/1009' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC(C(=O)[O-])=C(C)C=C2C)[N-]C1=O) `REAL300000237990.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237990 none COC1=CN=C(C=CC2=CC(C(=O)[O-])=C(C)C=C2C)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [50, 29, 29, 28, 28, 8, 8, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 29, 29, 29, 51, 51, 51, 29, 8, 8, 1, 2, 2, 2, 1, 2, 2, 2] 51 rigid atoms, others: [32, 7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 33, 34, 35]) total number of confs: 117 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237990 none COC1=CN=C(C=CC2=CC(C(=O)[O-])=C(C)C=C2C)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 29, 29, 29, 51, 51, 28, 28, 29, 29, 29, 1, 1, 1, 4, 4, 4, 1, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29] 51 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 154 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237990 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237990 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237990/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237990/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237990 Building REAL300000237991 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237991' /scratch/stefan/7769818/working/building/REAL300000237991 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237991 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237991/0 /scratch/stefan/7769818/working/building/REAL300000237991 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1010 `/scratch/stefan/7769818/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(OC(C)C(=O)[O-])C=C2)NC1=O) `REAL300000237991.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237991 none COC1=CN=C(C=CC2=CC=C(OC(C)C(=O)[O-])C=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 4, 4, 1, 1, 1, 1, 1, 1, 11, 31, 31, 46, 46, 1, 1, 25, 25, 25, 58, 58, 58, 25, 4, 4, 1, 1, 31, 31, 31, 31, 1, 1, 25] 201 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 37]) total number of confs: 243 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237991 none COC1=CN=C(C=CC2=CC=C(OC(C)C(=O)[O-])C=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 25, 25, 12, 12, 104, 184, 184, 201, 201, 25, 25, 1, 1, 1, 4, 4, 4, 1, 12, 12, 25, 25, 184, 184, 184, 184, 25, 25, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 26, 37] 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, 34, 35, 36]) total number of confs: 646 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237991 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237991/1 /scratch/stefan/7769818/working/building/REAL300000237991 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1011 `/scratch/stefan/7769818/working/3D/1011' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=C(OC(C)C(=O)[O-])C=C2)[N-]C1=O) `REAL300000237991.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237991 none COC1=CN=C(C=CC2=CC=C(OC(C)C(=O)[O-])C=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [44, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 1, 1, 12, 30, 30, 45, 45, 1, 1, 21, 21, 21, 44, 44, 44, 21, 4, 4, 1, 1, 30, 30, 30, 30, 1, 1] 174 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 213 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237991 none COC1=CN=C(C=CC2=CC=C(OC(C)C(=O)[O-])C=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 12, 12, 22, 22, 12, 12, 91, 143, 143, 174, 174, 22, 22, 1, 1, 1, 3, 3, 3, 1, 12, 12, 22, 22, 143, 143, 143, 143, 22, 22] 174 rigid atoms, others: [1, 2, 3, 4, 5, 6, 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, 34, 35, 36]) total number of confs: 549 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237991 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237991 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237991/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237991/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237991 Building REAL300000237992 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237992' /scratch/stefan/7769818/working/building/REAL300000237992 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237992 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237992/0 /scratch/stefan/7769818/working/building/REAL300000237992 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1012 `/scratch/stefan/7769818/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=CC=C2OCCC(=O)[O-])NC1=O) `REAL300000237992.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237992 none COC1=CN=C(C=CC2=CC=CC=C2OCCC(=O)[O-])NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 4, 7, 6, 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: [35, 25, 25, 25, 25, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 17, 26, 38, 36, 25, 25, 25, 35, 35, 35, 25, 9, 9, 1, 1, 1, 1, 18, 18, 26, 26, 25] 72 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 206 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237992 none COC1=CN=C(C=CC2=CC=CC=C2OCCC(=O)[O-])NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 12, 12, 25, 25, 19, 25, 25, 25, 44, 54, 62, 72, 70, 1, 1, 1, 3, 3, 3, 1, 12, 12, 25, 25, 25, 25, 54, 54, 62, 62, 1] 72 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 26, 37] 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, 34, 35, 36]) total number of confs: 246 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237992 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237992/1 /scratch/stefan/7769818/working/building/REAL300000237992 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1013 `/scratch/stefan/7769818/working/3D/1013' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=CC=C2OCCC(=O)[O-])[N-]C1=O) `REAL300000237992.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237992 none COC1=CN=C(C=CC2=CC=CC=C2OCCC(=O)[O-])[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [50, 27, 27, 27, 27, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 33, 42, 64, 53, 27, 27, 27, 50, 50, 50, 27, 9, 9, 1, 1, 1, 1, 33, 33, 42, 42] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 321 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237992 none COC1=CN=C(C=CC2=CC=CC=C2OCCC(=O)[O-])[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 13, 27, 27, 27, 93, 173, 176, 201, 201, 1, 1, 1, 3, 3, 3, 1, 7, 7, 27, 27, 27, 27, 173, 173, 176, 176] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 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, 34, 35, 36]) total number of confs: 717 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237992 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237992 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237992/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237992/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237992 Building REAL300000237993 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237993' /scratch/stefan/7769818/working/building/REAL300000237993 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237993 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237993/0 /scratch/stefan/7769818/working/building/REAL300000237993 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1014 `/scratch/stefan/7769818/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)NC1=O) `REAL300000237993.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237993 none COC1=CN=C(C=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 9, 22, 25, 25, 22, 26, 26, 22, 26, 26, 1, 28, 28, 28, 46, 46, 46, 28, 5, 5, 1, 1, 1, 22, 26, 26, 22, 26, 26, 1, 28] 201 rigid atoms, others: [34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 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, 44]) total number of confs: 172 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237993 none COC1=CN=C(C=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 198, 198, 198, 198, 75, 75, 26, 26, 26, 26, 26, 7, 3, 1, 3, 4, 4, 1, 1, 1, 1, 1, 1, 26, 198, 198, 198, 201, 201, 201, 198, 75, 75, 26, 26, 26, 3, 1, 1, 1, 1, 1, 26, 198] 201 rigid atoms, others: [38, 39, 40, 41, 42, 14, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44]) total number of confs: 364 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: REAL300000237993 none COC1=CN=C(C=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 28, 28, 28, 28, 28, 106, 193, 196, 196, 193, 198, 198, 193, 198, 198, 28, 1, 1, 1, 3, 3, 3, 1, 12, 12, 28, 28, 28, 193, 198, 198, 193, 198, 198, 28, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 44, 25, 26, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 651 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237993 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237993/1 /scratch/stefan/7769818/working/building/REAL300000237993 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1015 `/scratch/stefan/7769818/working/3D/1015' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)[N-]C1=O) `REAL300000237993.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237993 none COC1=CN=C(C=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 26, 26, 26, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 25, 30, 30, 25, 32, 32, 25, 32, 32, 1, 26, 26, 26, 37, 37, 37, 26, 6, 6, 1, 1, 1, 25, 32, 32, 25, 32, 32, 1] 201 rigid atoms, others: [34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 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: 192 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237993 none COC1=CN=C(C=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 188, 188, 188, 188, 90, 90, 32, 32, 32, 32, 32, 9, 3, 1, 3, 4, 4, 1, 1, 1, 1, 1, 1, 32, 188, 188, 188, 201, 201, 201, 188, 90, 90, 32, 32, 32, 3, 1, 1, 1, 1, 1, 32] 201 rigid atoms, others: [38, 39, 40, 41, 42, 14, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43]) total number of confs: 396 number of broken/clashed sets: 6 ./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: REAL300000237993 none COC1=CN=C(C=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 10, 10, 26, 26, 26, 26, 26, 96, 170, 185, 185, 170, 188, 188, 170, 188, 188, 26, 1, 1, 1, 3, 3, 3, 1, 10, 11, 26, 26, 26, 170, 188, 188, 170, 188, 188, 26] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 25, 26, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 660 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237993 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237993 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237993/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237993/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237993 Building REAL300000237994 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237994' /scratch/stefan/7769818/working/building/REAL300000237994 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237994 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237994/0 /scratch/stefan/7769818/working/building/REAL300000237994 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1016 `/scratch/stefan/7769818/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC=C(OC)C(=O)N2)C=C1C(=O)[O-]) `REAL300000237994.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237994 none COC1=CC=C(C=CC2=NC=C(OC)C(=O)N2)C=C1C(=O)[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', 'N.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 8, 1, 1, 12, 5, 1, 11, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 2, 2, 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: [73, 41, 41, 41, 41, 12, 12, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 41, 41, 41, 68, 68, 73, 73, 73, 41, 41, 12, 12, 1, 4, 4, 4, 1, 41] 98 rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34]) total number of confs: 241 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237994 none COC1=CC=C(C=CC2=NC=C(OC)C(=O)N2)C=C1C(=O)[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', 'N.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 1, 1, 1, 8, 1, 1, 12, 5, 1, 11, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 2, 2, 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, 6, 6, 41, 41, 41, 41, 68, 41, 41, 41, 1, 1, 1, 3, 3, 4, 4, 4, 1, 1, 6, 6, 41, 68, 68, 68, 41, 1] 98 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 17, 18, 19, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 118 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237994 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237994/1 /scratch/stefan/7769818/working/building/REAL300000237994 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1017 `/scratch/stefan/7769818/working/3D/1017' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC2=NC=C(OC)C(=O)[N-]2)C=C1C(=O)[O-]) `REAL300000237994.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237994 none COC1=CC=C(C=CC2=NC=C(OC)C(=O)[N-]2)C=C1C(=O)[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', 'N.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', '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, 1, 1, 1, 1, 8, 1, 1, 12, 5, 1, 11, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [52, 32, 32, 32, 32, 12, 12, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 32, 32, 32, 57, 57, 52, 52, 52, 32, 32, 12, 12, 1, 3, 3, 3, 32] 89 rigid atoms, others: [7, 8, 9, 10, 11, 12, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 196 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237994 none COC1=CC=C(C=CC2=NC=C(OC)C(=O)[N-]2)C=C1C(=O)[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', 'N.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', '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, 1, 1, 1, 1, 8, 1, 1, 12, 5, 1, 11, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 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: [3, 1, 1, 1, 1, 1, 1, 5, 5, 32, 32, 32, 32, 68, 32, 32, 32, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 5, 5, 32, 68, 68, 68, 1] 89 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 17, 18, 19, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237994 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237994 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237994/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237994/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237994 Building REAL300000237995 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237995' /scratch/stefan/7769818/working/building/REAL300000237995 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237995 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237995/0 /scratch/stefan/7769818/working/building/REAL300000237995 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1018 `/scratch/stefan/7769818/working/3D/1018' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC(C(=O)[O-])=C(OC)C=C2OC)NC1=O) `REAL300000237995.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237995 none COC1=CN=C(C=CC2=CC(C(=O)[O-])=C(OC)C=C2OC)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 1, 1, 12, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 66, 66, 66, 66, 9, 9, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 1, 1, 1, 3, 66, 66, 66, 109, 109, 109, 66, 9, 9, 1, 3, 3, 3, 1, 4, 4, 4, 66] 201 rigid atoms, others: [34, 7, 8, 9, 10, 11, 14, 15, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 181 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237995 none COC1=CN=C(C=CC2=CC(C(=O)[O-])=C(OC)C=C2OC)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 1, 1, 12, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 66, 66, 66, 114, 114, 66, 66, 108, 66, 66, 66, 89, 1, 1, 1, 4, 4, 4, 1, 13, 13, 66, 108, 108, 108, 66, 89, 89, 89, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 38, 21, 22, 23, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 423 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237995 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237995/1 /scratch/stefan/7769818/working/building/REAL300000237995 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1019 `/scratch/stefan/7769818/working/3D/1019' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC(C(=O)[O-])=C(OC)C=C2OC)[N-]C1=O) `REAL300000237995.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237995 none COC1=CN=C(C=CC2=CC(C(=O)[O-])=C(OC)C=C2OC)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 1, 1, 12, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 78, 78, 78, 78, 11, 11, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 1, 1, 1, 3, 78, 78, 78, 129, 129, 129, 78, 11, 11, 1, 4, 4, 4, 1, 4, 4, 4] 201 rigid atoms, others: [34, 7, 8, 9, 10, 11, 14, 15, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35, 36, 37]) total number of confs: 219 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237995 none COC1=CN=C(C=CC2=CC(C(=O)[O-])=C(OC)C=C2OC)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 1, 1, 12, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 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 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, 12, 12, 78, 78, 78, 119, 119, 78, 78, 123, 78, 78, 78, 103, 1, 1, 1, 3, 3, 3, 1, 12, 12, 78, 123, 123, 123, 78, 103, 103, 103] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 401 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237995 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237995 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237995/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237995/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237995 Building REAL300000237996 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237996' /scratch/stefan/7769818/working/building/REAL300000237996 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237996 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237996/0 /scratch/stefan/7769818/working/building/REAL300000237996 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1020 `/scratch/stefan/7769818/working/3D/1020' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC(Br)=CC(C(=O)[O-])=C2)NC1=O) `REAL300000237996.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237996 none COC1=CN=C(C=CC2=CC(Br)=CC(C(=O)[O-])=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 6, 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, 15, 15, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 16, 16, 16, 23, 23, 23, 16, 5, 5, 1, 1, 1, 16] 23 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 50 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237996 none COC1=CN=C(C=CC2=CC(Br)=CC(C(=O)[O-])=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 9, 15, 15, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 4, 4, 4, 1, 9, 9, 16, 16, 16, 1] 23 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 24, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 44 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237996 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237996/1 /scratch/stefan/7769818/working/building/REAL300000237996 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1021 `/scratch/stefan/7769818/working/3D/1021' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC(Br)=CC(C(=O)[O-])=C2)[N-]C1=O) `REAL300000237996.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237996 none COC1=CN=C(C=CC2=CC(Br)=CC(C(=O)[O-])=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 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, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 23, 23, 23, 23, 23, 23, 5, 5, 1, 1, 1] 23 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 37 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237996 none COC1=CN=C(C=CC2=CC(Br)=CC(C(=O)[O-])=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 3, 1, 10, 10, 23, 23, 23] 23 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 24] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 45 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237996 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237996 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237996/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237996/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237996 Building REAL300000237997 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237997' /scratch/stefan/7769818/working/building/REAL300000237997 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237997 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237997/0 /scratch/stefan/7769818/working/building/REAL300000237997 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1022 `/scratch/stefan/7769818/working/3D/1022' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC(F)=C(C(=O)[O-])C=C2F)NC1=O) `REAL300000237997.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237997 none COC1=CN=C(C=CC2=CC(F)=C(C(=O)[O-])C=C2F)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 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, 42, 42, 42, 42, 9, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 42, 42, 42, 55, 55, 55, 42, 9, 9, 1, 1, 42] 55 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 91 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237997 none COC1=CN=C(C=CC2=CC(F)=C(C(=O)[O-])C=C2F)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 12, 12, 42, 42, 42, 42, 42, 55, 55, 42, 42, 42, 1, 1, 1, 3, 3, 3, 1, 12, 12, 42, 42, 1] 55 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 25, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237997 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237997/1 /scratch/stefan/7769818/working/building/REAL300000237997 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1023 `/scratch/stefan/7769818/working/3D/1023' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CC(F)=C(C(=O)[O-])C=C2F)[N-]C1=O) `REAL300000237997.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237997 none COC1=CN=C(C=CC2=CC(F)=C(C(=O)[O-])C=C2F)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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, 42, 42, 42, 42, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 42, 42, 42, 47, 47, 47, 42, 12, 12, 1, 1] 47 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 79 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237997 none COC1=CN=C(C=CC2=CC(F)=C(C(=O)[O-])C=C2F)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 15, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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, 11, 11, 42, 42, 42, 42, 42, 47, 47, 42, 42, 42, 1, 1, 1, 4, 4, 4, 1, 11, 12, 42, 42] 47 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 94 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237997 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237997 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237997/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237997/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237997 Building REAL300000237998 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237998' /scratch/stefan/7769818/working/building/REAL300000237998 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000237998 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237998/0 /scratch/stefan/7769818/working/building/REAL300000237998 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1024 `/scratch/stefan/7769818/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CNC(C=CC2=C3C(=CC=C2)NN=C3C(=O)[O-])=NC1=O) `REAL300000237998.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237998 none COC1=CNC(C=CC2=C3C(=CC=C2)NN=C3C(=O)[O-])=NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 8, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 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, 19, 19, 19, 19, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 19, 21, 21, 21, 19, 19, 9, 9, 1, 1, 1, 1] 21 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237998 none COC1=CNC(C=CC2=C3C(=CC=C2)NN=C3C(=O)[O-])=NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 8, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 2, 2, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 21, 21, 1, 1, 1, 4, 4, 4, 1, 1, 9, 9, 19, 19, 19, 19] 21 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237998 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237998 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237998/0.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237998 Building REAL300000237999 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000237999' /scratch/stefan/7769818/working/building/REAL300000237999 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000237999 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000237999/0 /scratch/stefan/7769818/working/building/REAL300000237999 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1025 `/scratch/stefan/7769818/working/3D/1025' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)NC1=O) `REAL300000237999.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000237999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237999 none COC1=CN=C(C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 75, 75, 76, 76, 9, 9, 1, 1, 1, 1, 1, 6, 10, 10, 1, 1, 1, 6, 6, 1, 6, 6, 76, 76, 76, 137, 137, 137, 76, 9, 9, 1, 6, 6, 6, 6, 5, 6, 6, 76] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 259 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237999 none COC1=CN=C(C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 109, 109, 109, 109, 28, 28, 6, 6, 6, 6, 6, 20, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 169, 169, 169, 109, 28, 28, 6, 20, 20, 1, 1, 1, 1, 1, 109] 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]) total number of confs: 359 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: REAL300000237999 none COC1=CN=C(C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 75, 76, 76, 184, 186, 186, 76, 76, 76, 109, 109, 93, 109, 109, 1, 1, 1, 4, 4, 4, 1, 12, 12, 76, 184, 184, 109, 109, 109, 109, 109, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 23, 24, 25, 29] set([0, 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]) total number of confs: 733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237999 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000237999/1 /scratch/stefan/7769818/working/building/REAL300000237999 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1026 `/scratch/stefan/7769818/working/3D/1026' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)[N-]C1=O) `REAL300000237999.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000237999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000237999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237999 none COC1=CN=C(C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 58, 58, 58, 58, 11, 11, 1, 1, 1, 1, 1, 8, 14, 14, 1, 1, 1, 6, 6, 2, 6, 6, 58, 58, 58, 95, 95, 95, 58, 11, 11, 1, 8, 8, 6, 6, 5, 6, 6] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 216 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000237999 none COC1=CN=C(C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 98, 98, 98, 98, 28, 28, 6, 6, 6, 6, 6, 28, 47, 47, 6, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 141, 141, 141, 98, 28, 28, 6, 28, 28, 1, 1, 1, 1, 1] 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]) total number of confs: 388 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: REAL300000237999 none COC1=CN=C(C=CC2=CN(CC(=O)[O-])N=C2C2=CC=CC=C2)[N-]C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 58, 58, 58, 147, 153, 153, 58, 58, 58, 98, 98, 77, 98, 98, 1, 1, 1, 4, 4, 4, 1, 9, 9, 58, 147, 147, 98, 98, 98, 98, 98] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 23, 24, 25, 29] set([0, 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]) total number of confs: 661 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000237999 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000237999 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000237999/0.* 1: /scratch/stefan/7769818/working/building/REAL300000237999/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000237999 Building REAL300000238000 mkdir: created directory `/scratch/stefan/7769818/working/building/REAL300000238000' /scratch/stefan/7769818/working/building/REAL300000238000 /scratch/stefan/7769818/working /scratch/stefan/7769818 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000238000 mkdir: created directory `0' /scratch/stefan/7769818/working/building/REAL300000238000/0 /scratch/stefan/7769818/working/building/REAL300000238000 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 0 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1027 `/scratch/stefan/7769818/working/3D/1027' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2=NN(CC(=O)[O-])C=C2C=CC2=NC=C(OC)C(=O)N2)C=C1) `REAL300000238000.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000238000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000238000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000238000 none COC1=CC=C(C2=NN(CC(=O)[O-])C=C2C=CC2=NC=C(OC)C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 12, 5, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 11, 11, 1, 1, 1, 1, 1, 5, 9, 9, 1, 1, 1, 8, 8, 50, 50, 50, 50, 94, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 5, 5, 1, 8, 8, 50, 94, 94, 94, 50, 11, 11] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 211 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000238000 none COC1=CC=C(C2=NN(CC(=O)[O-])C=C2C=CC2=NC=C(OC)C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 12, 5, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 110, 147, 147, 50, 50, 50, 50, 50, 93, 134, 134, 50, 11, 11, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 147, 147, 147, 147, 147, 147, 147, 93, 93, 50, 11, 11, 1, 4, 4, 4, 1, 147, 147] 201 rigid atoms, others: [38, 42, 16, 17, 18, 19, 20, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 43, 44]) total number of confs: 770 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: REAL300000238000 none COC1=CC=C(C2=NN(CC(=O)[O-])C=C2C=CC2=NC=C(OC)C(=O)N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 12, 5, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 23, 36, 36, 11, 11, 11, 43, 43, 147, 147, 147, 147, 181, 147, 147, 147, 1, 1, 1, 2, 2, 1, 1, 23, 23, 11, 43, 43, 147, 181, 181, 181, 147, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 43, 44, 26, 27, 28, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 411 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000238000 /scratch/stefan/7769818/working /scratch/stefan/7769818 mkdir: created directory `1' /scratch/stefan/7769818/working/building/REAL300000238000/1 /scratch/stefan/7769818/working/building/REAL300000238000 /scratch/stefan/7769818/working /scratch/stefan/7769818 Protomer 1 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7769818/working/3D/1028 `/scratch/stefan/7769818/working/3D/1028' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2=NN(CC(=O)[O-])C=C2C=CC2=NC=C(OC)C(=O)[N-]2)C=C1) `REAL300000238000.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000238000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769818/working/building/REAL300000238000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000238000 none COC1=CC=C(C2=NN(CC(=O)[O-])C=C2C=CC2=NC=C(OC)C(=O)[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 12, 5, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 13, 13, 1, 1, 1, 9, 9, 40, 40, 40, 40, 65, 40, 40, 40, 11, 11, 11, 11, 11, 11, 11, 7, 7, 1, 9, 9, 40, 65, 65, 65, 11, 11] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000238000 none COC1=CC=C(C2=NN(CC(=O)[O-])C=C2C=CC2=NC=C(OC)C(=O)[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 12, 5, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 42, 40, 103, 103, 40, 40, 40, 40, 40, 110, 139, 139, 40, 8, 8, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 103, 103, 103, 103, 103, 103, 103, 110, 110, 40, 8, 8, 1, 3, 3, 3, 103, 103] 201 rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 760 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: REAL300000238000 none COC1=CC=C(C2=NN(CC(=O)[O-])C=C2C=CC2=NC=C(OC)C(=O)[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 12, 5, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 39, 60, 60, 11, 11, 11, 35, 35, 103, 103, 103, 103, 140, 103, 103, 103, 1, 1, 2, 2, 2, 1, 1, 39, 39, 11, 35, 35, 103, 140, 140, 140, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 42, 43, 26, 27, 31] set([7, 8, 9, 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: 433 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769818/working/building/REAL300000238000 /scratch/stefan/7769818/working /scratch/stefan/7769818 Finished preparing REAL300000238000 Recording results /scratch/stefan/7769818/working /scratch/stefan/7769818 Appending to /scratch/stefan/7769818/finished/xaaaajd.* 0: /scratch/stefan/7769818/working/building/REAL300000238000/0.* 1: /scratch/stefan/7769818/working/building/REAL300000238000/1.* Removing working files in /scratch/stefan/7769818/working/building/REAL300000238000 /scratch/stefan/7769818 Compressing combined databse files /scratch/stefan/7769818/finished/xaaaajd.db2.gz /scratch/stefan/7769818/finished/xaaaajd.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7769818/finished) ======================================================= Finalizing... removed `/scratch/stefan/7769818/working/3D/1029' removed directory: `/scratch/stefan/7769818/working/3D' `/scratch/stefan/7769818/working/protonate' -> `/scratch/stefan/7769818/archive' `/scratch/stefan/7769818/working/input-smiles.ism' -> `/scratch/stefan/7769818/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7769818/working/building' rmdir: removing directory, `/scratch/stefan/7769818/working' ls: No match. ls: No match.